.. _list_software: List of supported software ========================== EasyBuild |version| supports 1798 different software packages (incl. toolchains, bundles): :ref:`list_software_letter_a` - :ref:`list_software_letter_b` - :ref:`list_software_letter_c` - :ref:`list_software_letter_d` - :ref:`list_software_letter_e` - :ref:`list_software_letter_f` - :ref:`list_software_letter_g` - :ref:`list_software_letter_h` - :ref:`list_software_letter_i` - :ref:`list_software_letter_j` - :ref:`list_software_letter_k` - :ref:`list_software_letter_l` - :ref:`list_software_letter_m` - :ref:`list_software_letter_n` - :ref:`list_software_letter_o` - :ref:`list_software_letter_p` - :ref:`list_software_letter_q` - :ref:`list_software_letter_r` - :ref:`list_software_letter_s` - :ref:`list_software_letter_t` - :ref:`list_software_letter_u` - :ref:`list_software_letter_v` - :ref:`list_software_letter_w` - :ref:`list_software_letter_x` - :ref:`list_software_letter_y` - :ref:`list_software_letter_z` .. _list_software_letter_3: *3* --- :ref:`list_software_3to2_328` .. _list_software_3to2_328: *3to2* ++++++ lib3to2 is a set of fixers that are intended to backport code written for Python version 3.x into Python version 2.x. *homepage*: https://pypi.python.org/pypi/3to2 ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``1.1.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``1.1.1`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============================== .. _list_software_letter_4: *4* --- :ref:`list_software_4ti2_323` .. _list_software_4ti2_323: *4ti2* ++++++ A software package for algebraic, geometric and combinatorial problems on linear spaces *homepage*: https://4ti2.github.io/ ========= =============== version toolchain ========= =============== ``1.6.9`` ``intel/2018b`` ========= =============== .. _list_software_letter_a: *A* --- :ref:`list_software_ABAQUS_445` - :ref:`list_software_ABINIT_439` - :ref:`list_software_ABySS_418` - :ref:`list_software_ack_303` - :ref:`list_software_ACT_216` - :ref:`list_software_ACTC_283` - :ref:`list_software_ada_294` - :ref:`list_software_AdapterRemoval_1431` - :ref:`list_software_ADDA_266` - :ref:`list_software_ADF_203` - :ref:`list_software_adjustText_1072` - :ref:`list_software_ADMIXTURE_691` - :ref:`list_software_ADOL-C_400` - :ref:`list_software_Advisor_728` - :ref:`list_software_AFNI_286` - :ref:`list_software_AGFusion_764` - :ref:`list_software_aiohttp_761` - :ref:`list_software_ALADIN_425` - :ref:`list_software_Albacore_793` - :ref:`list_software_ALFA_276` - :ref:`list_software_alleleCount_1144` - :ref:`list_software_Allinea_694` - :ref:`list_software_ALLPATHS-LG_793` - :ref:`list_software_ALPS_304` - :ref:`list_software_Amara_482` - :ref:`list_software_amask_525` - :ref:`list_software_Amber_487` - :ref:`list_software_AmberMini_884` - :ref:`list_software_AmberTools_1016` - :ref:`list_software_AMD-LibM_611` - :ref:`list_software_AMD-RNG_486` - :ref:`list_software_AMD-SecureRNG_1101` - :ref:`list_software_AMOS_304` - :ref:`list_software_AMPL-MP_500` - :ref:`list_software_Anaconda2_839` - :ref:`list_software_Anaconda3_840` - :ref:`list_software_angsd_525` - :ref:`list_software_Annif_492` - :ref:`list_software_annovar_757` - :ref:`list_software_ANSYS_398` - :ref:`list_software_ANSYS_CFD_698` - :ref:`list_software_ant_323` - :ref:`list_software_ANTLR_385` - :ref:`list_software_ANTs_342` - :ref:`list_software_anvio_541` - :ref:`list_software_APBS_294` - :ref:`list_software_APR_227` - :ref:`list_software_APR-util_718` - :ref:`list_software_ARAGORN_522` - :ref:`list_software_Arb_277` - :ref:`list_software_ARCH_286` - :ref:`list_software_ARGoS_412` - :ref:`list_software_argtable_834` - :ref:`list_software_Armadillo_917` - :ref:`list_software_ARPACK++_520` - :ref:`list_software_arpack-ng_884` - :ref:`list_software_ArrayFire_901` - :ref:`list_software_Arriba_593` - :ref:`list_software_Arrow_523` - :ref:`list_software_ART_231` - :ref:`list_software_ARWEN_381` - :ref:`list_software_ASAP3_344` - :ref:`list_software_ASE_217` - :ref:`list_software_ASHS_303` - :ref:`list_software_Aspera-CLI_865` - :ref:`list_software_Aspera-Connect_1363` - :ref:`list_software_Assimulo_845` - :ref:`list_software_ASTRID_455` - :ref:`list_software_astropy_786` - :ref:`list_software_at-spi2-atk_1005` - :ref:`list_software_at-spi2-core_1110` - :ref:`list_software_ATK_224` - :ref:`list_software_ATLAS_373` - :ref:`list_software_atomate_747` - :ref:`list_software_AtomPAW_633` - :ref:`list_software_atools_658` - :ref:`list_software_ATSAS_380` - :ref:`list_software_attr_443` - :ref:`list_software_AUGUSTUS_641` - :ref:`list_software_Autoconf_831` - :ref:`list_software_Autoconf-archive_1614` - :ref:`list_software_AutoDock_794` - :ref:`list_software_AutoDock_Vina_1287` - :ref:`list_software_AutoGrid_799` - :ref:`list_software_Automake_823` - :ref:`list_software_Autotools_970` - :ref:`list_software_awscli_643` .. _list_software_ABAQUS_445: *ABAQUS* ++++++++ Finite Element Analysis software for modeling, visualization and best-in-class implicit and explicit dynamics FEA. *homepage*: http://www.simulia.com/products/abaqus_fea.html ========== ================= ========== version versionsuffix toolchain ========== ================= ========== ``6.12.1`` ``-linux-x86_64`` ``system`` ``6.13.5`` ``-linux-x86_64`` ``system`` ``6.14.1`` ``-linux-x86_64`` ``system`` ``2017`` ``-hotfix-1721`` ``system`` ``2018`` ``-hotfix-1806`` ``system`` ========== ================= ========== .. _list_software_ABINIT_439: *ABINIT* ++++++++ ABINIT is a package whose main program allows one to find the total energy, charge density and electronic structure of systems made of electrons and nuclei (molecules and periodic solids) within Density Functional Theory (DFT), using pseudopotentials and a planewave or wavelet basis. *homepage*: http://www.abinit.org/ ========== ======================== =============================== version versionsuffix toolchain ========== ======================== =============================== ``7.0.3`` ``-x86_64_linux_gnu4.5`` ``system`` ``7.0.5`` ``-x86_64_linux_gnu4.5`` ``system`` ``7.2.1`` ``-x86_64_linux_gnu4.5`` ``system`` ``7.10.5`` ``intel/2016.02-GCC-4.9`` ``7.10.5`` ``-libxc`` ``intel/2016.02-GCC-4.9`` ``8.0.8`` ``intel/2016a`` ``8.0.8b`` ``foss/2016b``, ``intel/2016b`` ``8.2.2`` ``foss/2016b``, ``intel/2016b`` ``8.4.4`` ``intel/2017b`` ``8.6.3`` ``intel/2018a`` ``8.10.2`` ``intel/2018b`` ``8.10.3`` ``intel/2018b`` ========== ======================== =============================== .. _list_software_ABySS_418: *ABySS* +++++++ Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler *homepage*: http://www.bcgsc.ca/platform/bioinfo/software/abyss ========= ================================================================ version toolchain ========= ================================================================ ``1.9.0`` ``foss/2016a`` ``2.0.2`` ``foss/2016b``, ``foss/2018a``, ``gompi/2019a``, ``intel/2016b`` ``2.0.3`` ``foss/2017b``, ``intel/2017b`` ========= ================================================================ .. _list_software_ack_303: *ack* +++++ ack is a tool like grep, optimized for programmers *homepage*: http://beyondgrep.com/ ======== ========== version toolchain ======== ========== ``2.14`` ``system`` ======== ========== .. _list_software_ACT_216: *ACT* +++++ ACT is a Java application for displaying pairwise comparisons between two or more DNA sequences. It can be used to identify and analyse regions of similarity and difference between genomes and to explore conservation of synteny, in the context of the entire sequences and their annotation. It can read complete EMBL, GENBANK and GFF entries or sequences in FASTA or raw format. *homepage*: https://sanger-pathogens.github.io/Artemis/ACT/ ========== ============= ========== version versionsuffix toolchain ========== ============= ========== ``18.0.2`` ``-Java-11`` ``system`` ``18.0.3`` ``-Java-11`` ``system`` ========== ============= ========== .. _list_software_ACTC_283: *ACTC* ++++++ ACTC converts independent triangles into triangle strips or fans. *homepage*: https://sourceforge.net/projects/actc ======= ===================================================== version toolchain ======= ===================================================== ``1.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``intel/2016b`` ======= ===================================================== .. _list_software_ada_294: *ada* +++++ Performs discrete, real, and gentle boost under both exponential and logistic loss on a given data set. *homepage*: https://cran.r-project.org/web/packages/ada/index.html ========= ============= =============== version versionsuffix toolchain ========= ============= =============== ``2.0-5`` ``-R-3.4.0`` ``intel/2017a`` ========= ============= =============== .. _list_software_AdapterRemoval_1431: *AdapterRemoval* ++++++++++++++++ AdapterRemoval searches for and removes remnant adapter sequences from High-Throughput Sequencing (HTS) data and (optionally) trims low quality bases from the 3' end of reads following adapter removal. *homepage*: https://github.com/%/(github_account)s/%(namelower)s ========= ============== version toolchain ========= ============== ``2.2.0`` ``foss/2016b`` ``2.2.2`` ``foss/2018b`` ``2.3.1`` ``foss/2018b`` ========= ============== .. _list_software_ADDA_266: *ADDA* ++++++ ADDA is an open-source parallel implementation of the discrete dipole approximation, capable to simulate light scattering by particles of arbitrary shape and composition in a wide range of particle sizes. *homepage*: https://github.com/adda-team/adda/wiki ========= ============== version toolchain ========= ============== ``1.3b4`` ``foss/2019a`` ========= ============== .. _list_software_ADF_203: *ADF* +++++ ADF is an accurate, parallelized, powerful computational chemistry program to understand and predict chemical structure and reactivity with density functional theory (DFT). *homepage*: http://www.scm.com/ADF/ ================================ =============== version toolchain ================================ =============== ``2009.01a.pc64_linux.intelmpi`` ``system`` ``2014.02`` ``system`` ``2014.11.r48287`` ``intel/2016a`` ``2016.101`` ``system`` ================================ =============== .. _list_software_adjustText_1072: *adjustText* ++++++++++++ A small library for automatically adjustment of text position in matplotlib plots to minimize overlaps. *homepage*: https://github.com/Phlya/adjustText ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``0.7.3`` ``-Python-3.7.2`` ``intel/2019a`` ========= ================= =============== .. _list_software_ADMIXTURE_691: *ADMIXTURE* +++++++++++ ADMIXTURE is a software tool for maximum likelihood estimation of individual ancestries from multilocus SNP genotype datasets. It uses the same statistical model as STRUCTURE but calculates estimates much more rapidly using a fast numerical optimization algorithm. *homepage*: http://software.genetics.ucla.edu/admixture ========= ========== version toolchain ========= ========== ``1.3.0`` ``system`` ========= ========== .. _list_software_ADOL-C_400: *ADOL-C* ++++++++ The package ADOL-C (Automatic Differentiation by OverLoading in C++) facilitates the evaluation of first and higher derivatives of vector functions that are defined by computer programs written in C or C++. The resulting derivative evaluation routines may be called from C/C++, Fortran, or any other language that can be linked with C. *homepage*: https://projects.coin-or.org/ADOL-C ========= =============== version toolchain ========= =============== ``2.7.0`` ``gompi/2019a`` ========= =============== .. _list_software_Advisor_728: *Advisor* +++++++++ Vectorization Optimization and Thread Prototyping - Vectorize & thread code or performance “dies” - Easy workflow + data + tips = faster code faster - Prioritize, Prototype & Predict performance gain *homepage*: https://software.intel.com/intel-advisor-xe ================ ========== version toolchain ================ ========== ``2016_update2`` ``system`` ``2017_update1`` ``system`` ``2018_update1`` ``system`` ``2018_update3`` ``system`` ``2019_update2`` ``system`` ``2019_update3`` ``system`` ``2019_update5`` ``system`` ================ ========== .. _list_software_AFNI_286: *AFNI* ++++++ AFNI is a set of C programs for processing, analyzing, and displaying functional MRI (FMRI) data - a technique for mapping human brain activity. *homepage*: http://afni.nimh.nih.gov/ ============ ================== =============================== version versionsuffix toolchain ============ ================== =============================== ``18.1.09`` ``-Python-3.6.4`` ``intel/2018a`` ``18.3.00`` ``-Python-3.6.6`` ``foss/2018b`` ``19.0.01`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``20160329`` ``-Python-2.7.11`` ``intel/2016a`` ============ ================== =============================== .. _list_software_AGFusion_764: *AGFusion* ++++++++++ AGFusion is a python package for annotating gene fusions from the human or mouse genomes. *homepage*: https://github.com/murphycj/AGFusion ======= ================= ============== version versionsuffix toolchain ======= ================= ============== ``1.2`` ``-Python-3.7.2`` ``foss/2019a`` ======= ================= ============== .. _list_software_aiohttp_761: *aiohttp* +++++++++ " Async http client/server framework *homepage*: https://github.com/aio-libs/aiohttp ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``3.5.4`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== .. _list_software_ALADIN_425: *ALADIN* ++++++++ ALADIN was entirely built on the notion of compatibility with its mother system, IFS/ARPEG. The latter, a joint development between the European Centre for Medium-Range Weather Forecasts (ECMWF) and Meteo-France, was only meant to consider global Numerical Weather Prediction applications; hence the idea, for ALADIN, to complement the IFS/ARPEGE project with a limited area model (LAM) version, while keeping the differences between the two softwares as small as possible. *homepage*: http://www.cnrm.meteo.fr/aladin/ =============== =============== version toolchain =============== =============== ``36t1_op2bf1`` ``intel/2016a`` =============== =============== .. _list_software_Albacore_793: *Albacore* ++++++++++ Albacore is a software project that provides an entry point to the Oxford Nanopore basecalling algorithms. *homepage*: https://community.nanoporetech.com/protocols/albacore-offline-basecalli/v/abec_2003_v1_revz_29nov2016 ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``2.0.2`` ``-Python-3.6.1`` ``intel/2017a`` ========= ================= =============== .. _list_software_ALFA_276: *ALFA* ++++++ ALFA provides a global overview of features distribution composing NGS dataset(s). Given a set of aligned reads (BAM files) and an annotation file (GTF format), the tool produces plots of the raw and normalized distributions of those reads among genomic categories (stop codon, 5'-UTR, CDS, intergenic, etc.) and biotypes (protein coding genes, miRNA, tRNA, etc.). Whatever the sequencing technique, whatever the organism. *homepage*: https://github.com/biocompibens/ALFA ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``1.1.1`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================= ============== .. _list_software_alleleCount_1144: *alleleCount* +++++++++++++ The alleleCount package primarily exists to prevent code duplication between some other projects, specifically AscatNGS and Battenberg. As of v4 the perl code wraps the C implementation of allele counting code for BAM/CRAM processing. *homepage*: http://cancerit.github.io/alleleCount/ ========= ================= version toolchain ========= ================= ``4.0.0`` ``GCCcore/6.4.0`` ========= ================= .. _list_software_Allinea_694: *Allinea* +++++++++ The Allinea environment is an essential toolkit for developers and computational scientists looking to get results faster. *homepage*: http://www.allinea.com =============================== ========== version toolchain =============================== ========== ``4.1-32834-Redhat-5.7-x86_64`` ``system`` ``4.1-32834-Redhat-6.0-x86_64`` ``system`` ``6.1.1-Ubuntu-14.04-x86_64`` ``system`` =============================== ========== .. _list_software_ALLPATHS-LG_793: *ALLPATHS-LG* +++++++++++++ ALLPATHS-LG, the new short read genome assembler. *homepage*: http://www.broadinstitute.org/software/allpaths-lg/blog/ ========= ============== version toolchain ========= ============== ``52488`` ``foss/2016a`` ========= ============== .. _list_software_ALPS_304: *ALPS* ++++++ The ALPS project (Algorithms and Libraries for Physics Simulations) is an open source effort aiming at providing high-end simulation codes for strongly correlated quantum mechanical systems as well as C++ libraries for simplifying the development of such code. *homepage*: http://alps.comp-phys.org/ ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``2.2.b4`` ``-Python-2.7.11`` ``intel/2016a`` ``2.3.0`` ``-Python-2.7.12`` ``foss/2016b`` ``2.3.0`` ``-Python-3.5.2`` ``foss/2016b`` ========== ================== =============== .. _list_software_Amara_482: *Amara* +++++++ Library for XML processing in Python, designed to balance the native idioms of Python with the native character of XML. *homepage*: https://pypi.org/project/Amara =========== ================== =============================== version versionsuffix toolchain =========== ================== =============================== ``1.2.0.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` =========== ================== =============================== .. _list_software_amask_525: *amask* +++++++ amask is a set of tools to to determine the affinity of MPI processes and OpenMP threads in a parallel environment. *homepage*: https://github.com/TACC/amask ============ ============== version toolchain ============ ============== ``20171106`` ``foss/2018a`` ``20190404`` ``foss/2018b`` ============ ============== .. _list_software_Amber_487: *Amber* +++++++ Amber (originally Assisted Model Building with Energy Refinement) is software for performing molecular dynamics and structure prediction. *homepage*: http://ambermd.org/amber.html ======= ================================================= ======================================================================== version versionsuffix toolchain ======= ================================================= ======================================================================== ``14`` ``-AmberTools-15-patchlevel-13-13`` ``intel/2016a`` ``16`` ``-AmberTools-16-patchlevel-5-14`` ``iomkl/2016.07`` ``16`` ``-AmberTools-16-patchlevel-5-14-CUDA`` ``iomkl/2016.09-GCC-4.9.3-2.25`` ``16`` ``-AmberTools-16-patchlevel-5-14-serial`` ``iomkl/2016.07`` ``16`` ``-AmberTools-17-patchlevel-10-15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``16`` ``-AmberTools-17-patchlevel-10-15-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``16`` ``-AmberTools-17-patchlevel-8-12`` ``intel/2017b`` ``18`` ``-AmberTools-18-patchlevel-10-8`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017b`` ======= ================================================= ======================================================================== .. _list_software_AmberMini_884: *AmberMini* +++++++++++ A stripped-down set of just antechamber, sqm, and tleap. *homepage*: https://github.com/choderalab/ambermini =========== =============== version toolchain =========== =============== ``16.16.0`` ``intel/2017b`` =========== =============== .. _list_software_AmberTools_1016: *AmberTools* ++++++++++++ AmberTools consists of several independently developed packages that work well by themselves, and with Amber itself. The suite can also be used to carry out complete molecular dynamics simulations, with either explicit water or generalized Born solvent models. *homepage*: http://ambermd.org/ ======= ================================ version toolchain ======= ================================ ``17`` ``intel/2017b``, ``intel/2018a`` ======= ================================ .. _list_software_AMD-LibM_611: *AMD-LibM* ++++++++++ AMD LibM is a software library containing a collection of basic math functions optimized for x86-64 processor based machines. *homepage*: https://developer.amd.com/amd-cpu-libraries/amd-math-library-libm/ ========= ================== version toolchain ========= ================== ``3.2.2`` ``GCC/7.3.0-2.30`` ========= ================== .. _list_software_AMD-RNG_486: *AMD-RNG* +++++++++ AMD Random Number Generator Library is a pseudorandom number generator library. *homepage*: https://developer.amd.com/amd-cpu-libraries/rng-library/ ======= ================== version toolchain ======= ================== ``1.0`` ``GCC/7.3.0-2.30`` ======= ================== .. _list_software_AMD-SecureRNG_1101: *AMD-SecureRNG* +++++++++++++++ The AMD Secure Random Number Generator (RNG) is a library that provides APIs to access the cryptographically secure random numbers generated by AMD’s hardware-based random number generator implementation. *homepage*: https://developer.amd.com/amd-cpu-libraries/rng-library/ ======= ================== version toolchain ======= ================== ``1.0`` ``GCC/7.3.0-2.30`` ======= ================== .. _list_software_AMOS_304: *AMOS* ++++++ The AMOS consortium is committed to the development of open-source whole genome assembly software *homepage*: http://amos.sourceforge.net ========= ============== version toolchain ========= ============== ``3.1.0`` ``foss/2018b`` ========= ============== .. _list_software_AMPL-MP_500: *AMPL-MP* +++++++++ An open-source library for mathematical programming. *homepage*: https://github.com/ampl/mp ========= ================= version toolchain ========= ================= ``3.1.0`` ``GCCcore/6.4.0`` ========= ================= .. _list_software_Anaconda2_839: *Anaconda2* +++++++++++ Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. *homepage*: https://www.anaconda.com =========== ========== version toolchain =========== ========== ``4.0.0`` ``system`` ``4.2.0`` ``system`` ``4.4.0`` ``system`` ``5.0.1`` ``system`` ``5.1.0`` ``system`` ``5.3.0`` ``system`` ``2018.12`` ``system`` ``2019.03`` ``system`` ``2019.07`` ``system`` ``2019.10`` ``system`` =========== ========== .. _list_software_Anaconda3_840: *Anaconda3* +++++++++++ Built to complement the rich, open source Python community, the Anaconda platform provides an enterprise-ready data analytics platform that empowers companies to adopt a modern open data science analytics architecture. *homepage*: https://www.anaconda.com =========== ========== version toolchain =========== ========== ``4.0.0`` ``system`` ``4.2.0`` ``system`` ``4.4.0`` ``system`` ``5.0.1`` ``system`` ``5.1.0`` ``system`` ``5.3.0`` ``system`` ``2018.12`` ``system`` ``2019.03`` ``system`` ``2019.07`` ``system`` ``2019.10`` ``system`` =========== ========== .. _list_software_angsd_525: *angsd* +++++++ Program for analysing NGS data. *homepage*: http://www.popgen.dk/angsd ========= ============== version toolchain ========= ============== ``0.910`` ``foss/2016a`` ``0.921`` ``foss/2018a`` ``0.925`` ``foss/2018b`` ========= ============== .. _list_software_Annif_492: *Annif* +++++++ Annif is a multi-algorithm automated subject indexing tool for libraries, archives and museums. *homepage*: https://github.com/NatLibFi/Annif ========== ================= =============================== version versionsuffix toolchain ========== ================= =============================== ``0.40.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ========== ================= =============================== .. _list_software_annovar_757: *annovar* +++++++++ ANNOVAR is an efficient software tool to utilize update-to-date information to functionally annotate genetic variants detected from diverse genomes (including human genome hg18, hg19, hg38, as well as mouse, worm, fly, yeast and many others). *homepage*: http://annovar.openbioinformatics.org/en/latest/ ============= ================ ============== version versionsuffix toolchain ============= ================ ============== ``2016Feb01`` ``-Perl-5.22.1`` ``foss/2016a`` ============= ================ ============== .. _list_software_ANSYS_398: *ANSYS* +++++++ ANSYS simulation software enables organizations to confidently predict how their products will operate in the real world. We believe that every product is a promise of something greater. *homepage*: http://www.ansys.com ======== ========== version toolchain ======== ========== ``15.0`` ``system`` ======== ========== .. _list_software_ANSYS_CFD_698: *ANSYS_CFD* +++++++++++ ANSYS computational fluid dynamics (CFD) simulation software allows you to predict, with confidence, the impact of fluid flows on your product throughout design and manufacturing as well as during end use. ANSYS renowned CFD analysis tools include the widely used and well-validated ANSYS Fluent and ANSYS CFX. *homepage*: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics ======== ========== version toolchain ======== ========== ``16.2`` ``system`` ``17.0`` ``system`` ======== ========== .. _list_software_ant_323: *ant* +++++ Apache Ant is a Java library and command-line tool whose mission is to drive processes described in build files as targets and extension points dependent upon each other. The main known usage of Ant is the build of Java applications. *homepage*: http://ant.apache.org/ ========== =================== ========== version versionsuffix toolchain ========== =================== ========== ``1.8.4`` ``-Java-1.7.0_10`` ``system`` ``1.8.4`` ``-Java-1.7.0_21`` ``system`` ``1.9.0`` ``-Java-1.7.0_15`` ``system`` ``1.9.0`` ``-Java-1.7.0_21`` ``system`` ``1.9.3`` ``-Java-1.7.0_60`` ``system`` ``1.9.3`` ``-Java-1.7.0_79`` ``system`` ``1.9.6`` ``-Java-1.7.0_75`` ``system`` ``1.9.6`` ``-Java-1.7.0_79`` ``system`` ``1.9.6`` ``-Java-1.7.0_80`` ``system`` ``1.9.6`` ``-Java-1.8.0_66`` ``system`` ``1.9.6`` ``-Java-1.8.0_72`` ``system`` ``1.9.6`` ``-Java-1.8.0_77`` ``system`` ``1.9.7`` ``-Java-1.8.0_92`` ``system`` ``1.10.0`` ``-Java-1.8.0_112`` ``system`` ``1.10.1`` ``-Java-1.8`` ``system`` ``1.10.1`` ``-Java-1.8.0_121`` ``system`` ``1.10.1`` ``-Java-1.8.0_144`` ``system`` ``1.10.1`` ``-Java-1.8.0_152`` ``system`` ``1.10.1`` ``-Java-1.8.0_162`` ``system`` ``1.10.5`` ``-Java-1.8`` ``system`` ``1.10.6`` ``-Java-1.8`` ``system`` ``1.10.7`` ``-Java-11`` ``system`` ========== =================== ========== .. _list_software_ANTLR_385: *ANTLR* +++++++ ANTLR, ANother Tool for Language Recognition, (formerly PCCTS) is a language tool that provides a framework for constructing recognizers, compilers, and translators from grammatical descriptions containing Java, C#, C++, or Python actions. *homepage*: http://www.antlr2.org/ ========= ================== ===================================================================================================== version versionsuffix toolchain ========= ================== ===================================================================================================== ``2.7.7`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018b``, ``foss/2019a``, ``intel/2017b`` ``2.7.7`` ``-Python-2.7.11`` ``foss/2016a`` ``2.7.7`` ``-Python-2.7.13`` ``intel/2017a`` ``2.7.7`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` ``2.7.7`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================== ===================================================================================================== .. _list_software_ANTs_342: *ANTs* ++++++ ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data. *homepage*: http://stnava.github.io/ANTs/ ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``2.2.0`` ``-Python-2.7.12`` ``foss/2016b`` ``2.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2.3.1`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================== =============================== .. _list_software_anvio_541: *anvio* +++++++ An analysis and visualization platform for 'omics data. *homepage*: https://merenlab.org/software/anvio/ ======= ================= =============== version versionsuffix toolchain ======= ================= =============== ``6.1`` ``-Python-3.7.4`` ``intel/2019b`` ======= ================= =============== .. _list_software_APBS_294: *APBS* ++++++ APBS is a software package for modeling biomolecular solvation through solution of the Poisson-Boltzmann equation (PBE), one of the most popular continuum models for describing electrostatic interactions between molecular solutes in salty, aqueous media. *homepage*: http://www.poissonboltzmann.org/apbs ======= ======================== ========== version versionsuffix toolchain ======= ======================== ========== ``1.4`` ``-linux-static-x86_64`` ``system`` ======= ======================== ========== .. _list_software_APR_227: *APR* +++++ Apache Portable Runtime (APR) libraries. *homepage*: http://apr.apache.org/ ========= ===================================================== version toolchain ========= ===================================================== ``1.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``iomkl/2018a`` ``1.7.0`` ``GCCcore/8.2.0`` ========= ===================================================== .. _list_software_APR-util_718: *APR-util* ++++++++++ Apache Portable Runtime (APR) util libraries. *homepage*: http://apr.apache.org/ ========= ======================================================================== version toolchain ========= ======================================================================== ``1.6.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``iomkl/2018a`` ========= ======================================================================== .. _list_software_ARAGORN_522: *ARAGORN* +++++++++ a program to detect tRNA genes and tmRNA genes in nucleotide sequences *homepage*: http://mbio-serv2.mbioekol.lu.se/ARAGORN/ ========== ============== version toolchain ========== ============== ``1.2.38`` ``foss/2016b`` ========== ============== .. _list_software_Arb_277: *Arb* +++++ Arb is a C library for arbitrary-precision interval arithmetic. It has full support for both real and complex numbers. The library is thread-safe, portable, and extensively tested. *homepage*: http://arblib.org ========== ========================================================== version toolchain ========== ========================================================== ``2.16.0`` ``GCC/7.3.0-2.30``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` ========== ========================================================== .. _list_software_ARCH_286: *ARCH* ++++++ Autoregressive Conditional Heteroskedasticity (ARCH) and other tools for financial econometrics, written in Python (with Cython and/or Numba used to improve performance). *homepage*: https://pypi.org/project/arch ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``4.5.0`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== .. _list_software_ARGoS_412: *ARGoS* +++++++ A parallel, multi-engine simulator for heterogeneous swarm robotics *homepage*: http://www.argos-sim.info ================ ============== ============== version versionsuffix toolchain ================ ============== ============== ``3.0.0-beta53`` ``-Lua-5.2.4`` ``foss/2018b`` ================ ============== ============== .. _list_software_argtable_834: *argtable* ++++++++++ Argtable is an ANSI C library for parsing GNU style command line options with a minimum of fuss. *homepage*: http://argtable.sourceforge.net/ ======== =================================================================================== version toolchain ======== =================================================================================== ``2.13`` ``GCCcore/8.2.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` ======== =================================================================================== .. _list_software_Armadillo_917: *Armadillo* +++++++++++ Armadillo is an open-source C++ linear algebra library (matrix maths) aiming towards a good balance between speed and ease of use. Integer, floating point and complex numbers are supported, as well as a subset of trigonometric and statistics functions. *homepage*: https://arma.sourceforge.net/ =========== ================== =============================== version versionsuffix toolchain =========== ================== =============================== ``7.600.2`` ``-Python-2.7.12`` ``foss/2016b`` ``7.800.0`` ``-Python-2.7.12`` ``intel/2016b`` ``7.950.1`` ``-Python-2.7.12`` ``intel/2016b`` ``8.300.1`` ``foss/2017b``, ``intel/2017b`` ``8.400.0`` ``foss/2018a`` ``9.700.2`` ``foss/2019a`` =========== ================== =============================== .. _list_software_ARPACK++_520: *ARPACK++* ++++++++++ Arpackpp is a C++ interface to the ARPACK Fortran package, which implements the implicit restarted Arnoldi method for iteratively solving large-scale sparse eigenvalue problems. *homepage*: https://github.com/m-reuter/arpackpp ============== ============== version toolchain ============== ============== ``2018.03.26`` ``foss/2017b`` ============== ============== .. _list_software_arpack-ng_884: *arpack-ng* +++++++++++ ARPACK is a collection of Fortran77 subroutines designed to solve large scale eigenvalue problems. *homepage*: https://github.com/opencollab/arpack-ng ========= ================================================================================ version toolchain ========= ================================================================================ ``3.3.0`` ``foss/2016a``, ``intel/2016a`` ``3.4.0`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b``, ``intel/2017a`` ``3.5.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b`` ``3.6.2`` ``intel/2018a`` ``3.7.0`` ``foss/2019a``, ``foss/2019b`` ========= ================================================================================ .. _list_software_ArrayFire_901: *ArrayFire* +++++++++++ ArrayFire is a general-purpose library that simplifies the process of developing software that targets parallel and massively-parallel architectures including CPUs, GPUs, and other hardware acceleration devices. *homepage*: https://arrayfire.com/ ========= ================ ============== version versionsuffix toolchain ========= ================ ============== ``3.6.4`` ``foss/2018b`` ``3.6.4`` ``-CUDA-9.2.88`` ``foss/2018b`` ========= ================ ============== .. _list_software_Arriba_593: *Arriba* ++++++++ Arriba is a command-line tool for the detection of gene fusions from RNA-Seq data. It was developed for the use in a clinical research setting. Therefore, short runtimes and high sensitivity were important design criteria. *homepage*: https://github.com/suhrig/arriba ========= ============== version toolchain ========= ============== ``1.1.0`` ``foss/2018b`` ========= ============== .. _list_software_Arrow_523: *Arrow* +++++++ Apache Arrow is a cross-language development platform for in-memory data. *homepage*: https://arrow.apache.org ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``0.7.1`` ``-Python-3.6.3`` ``intel/2017b`` ``0.12.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``0.12.0`` ``-Python-3.6.6`` ``intel/2018b`` ========== ================== =============================== .. _list_software_ART_231: *ART* +++++ ART is a set of simulation tools to generate synthetic next-generation sequencing reads *homepage*: http://www.niehs.nih.gov/research/resources/software/biostatistics/art/ ============== ================================== version toolchain ============== ================================== ``2016.06.05`` ``GCCcore/6.4.0``, ``intel/2016b`` ============== ================================== .. _list_software_ARWEN_381: *ARWEN* +++++++ ARWEN, tRNA detection in metazoan mitochondrial sequences *homepage*: http://mbio-serv2.mbioekol.lu.se/ARWEN ========= ================= version toolchain ========= ================= ``1.2.3`` ``GCCcore/7.3.0`` ========= ================= .. _list_software_ASAP3_344: *ASAP3* +++++++ ASAP is a calculator for doing large-scale classical molecular dynamics within the Campos Atomic Simulation Environment (ASE). *homepage*: https://wiki.fysik.dtu.dk/asap/ =========== ================= ================================================ version versionsuffix toolchain =========== ================= ================================================ ``3.10.7`` ``-Python-3.5.2`` ``foss/2016b`` ``3.10.7`` ``-Python-3.6.2`` ``foss/2017b`` ``3.10.8`` ``-Python-3.5.2`` ``foss/2016b`` ``3.10.8`` ``-Python-3.6.2`` ``foss/2017b`` ``3.10.8`` ``-Python-3.6.3`` ``foss/2017b`` ``3.10.10`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.11.10`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` =========== ================= ================================================ .. _list_software_ASE_217: *ASE* +++++ ASE is a python package providing an open source Atomic Simulation Environment in the Python scripting language. *homepage*: https://wiki.fysik.dtu.dk/ase/ ============== ================== ================================================ version versionsuffix toolchain ============== ================== ================================================ ``3.9.1.4567`` ``-Python-2.7.11`` ``intel/2016a`` ``3.10.0`` ``-Python-2.7.11`` ``intel/2016.02-GCC-4.9`` ``3.11.0`` ``-Python-2.7.12`` ``intel/2016b`` ``3.13.0`` ``-Python-2.7.12`` ``foss/2016b`` ``3.13.0`` ``-Python-2.7.13`` ``intel/2017a`` ``3.15.0`` ``-Python-2.7.12`` ``foss/2016b`` ``3.15.0`` ``-Python-2.7.14`` ``intel/2017b`` ``3.15.0`` ``-Python-3.5.2`` ``foss/2016b`` ``3.15.0`` ``-Python-3.6.2`` ``foss/2017b`` ``3.15.0`` ``-Python-3.6.3`` ``foss/2017b`` ``3.16.2`` ``-Python-3.6.4`` ``iomkl/2018.02``, ``iomkl/2018a`` ``3.16.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.17.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.17.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``3.18.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.18.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ============== ================== ================================================ .. _list_software_ASHS_303: *ASHS* ++++++ Automatic Segmentation of Hippocampal Subfields (ASHS) *homepage*: https://sites.google.com/site/hipposubfields/home =================== ========== version toolchain =================== ========== ``rev103_20140612`` ``system`` =================== ========== .. _list_software_Aspera-CLI_865: *Aspera-CLI* ++++++++++++ IBM Aspera Command-Line Interface (the Aspera CLI) is a collection of Aspera tools for performing high-speed, secure data transfers from the command line. The Aspera CLI is for users and organizations who want to automate their transfer workflows. *homepage*: http://asperasoft.com ========= ================= ========== version versionsuffix toolchain ========= ================= ========== ``3.7.2`` ``.354.010c3b8`` ``system`` ``3.9.0`` ``.1326.6985b21`` ``system`` ========= ================= ========== .. _list_software_Aspera-Connect_1363: *Aspera-Connect* ++++++++++++++++ Connect is an install-on-demand Web browser plug-in that facilitates high-speed uploads and downloads with an Aspera transfer server. *homepage*: http://downloads.asperasoft.com/connect2/ ========= ========== version toolchain ========= ========== ``3.6.1`` ``system`` ``3.9.6`` ``system`` ========= ========== .. _list_software_Assimulo_845: *Assimulo* ++++++++++ Assimulo is a simulation package for solving ordinary differential equations. *homepage*: https://jmodelica.org/assimulo/ ======= ================== =============== version versionsuffix toolchain ======= ================== =============== ``2.9`` ``-Python-2.7.15`` ``intel/2018b`` ======= ================== =============== .. _list_software_ASTRID_455: *ASTRID* ++++++++ ASTRID-2 is a method for estimating species trees from gene trees. *homepage*: https://github.com/pranjalv123/ASTRID ========= =============== version toolchain ========= =============== ``2.2.1`` ``gompi/2019a`` ========= =============== .. _list_software_astropy_786: *astropy* +++++++++ The Astropy Project is a community effort to develop a single core package for Astronomy in Python and foster interoperability between Python astronomy packages. *homepage*: http://www.astropy.org/ ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``2.0.12`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.0.14`` ``foss/2019a`` ========== ================== =============================== .. _list_software_at-spi2-atk_1005: *at-spi2-atk* +++++++++++++ AT-SPI 2 toolkit bridge *homepage*: https://wiki.gnome.org/Accessibility ========== ================== version toolchain ========== ================== ``2.26.3`` ``fosscuda/2018b`` ``2.32.0`` ``GCCcore/8.2.0`` ========== ================== .. _list_software_at-spi2-core_1110: *at-spi2-core* ++++++++++++++ Assistive Technology Service Provider Interface. *homepage*: https://wiki.gnome.org/Accessibility ========== ================== version toolchain ========== ================== ``2.26.3`` ``fosscuda/2018b`` ``2.32.0`` ``GCCcore/8.2.0`` ========== ================== .. _list_software_ATK_224: *ATK* +++++ ATK provides the set of accessibility interfaces that are implemented by other toolkits and applications. Using the ATK interfaces, accessibility tools have full access to view and control running applications. *homepage*: https://developer.gnome.org/ATK/stable/ ========== =================================================================== version toolchain ========== =================================================================== ``2.18.0`` ``intel/2016a`` ``2.20.0`` ``foss/2016a``, ``intel/2016a`` ``2.22.0`` ``foss/2016b``, ``intel/2016b`` ``2.26.0`` ``intel/2017a`` ``2.26.1`` ``foss/2018b``, ``intel/2017b`` ``2.27.1`` ``foss/2017b``, ``intel/2017b`` ``2.28.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a`` ``2.32.0`` ``GCCcore/8.2.0`` ========== =================================================================== .. _list_software_ATLAS_373: *ATLAS* +++++++ ATLAS (Automatically Tuned Linear Algebra Software) is the application of the AEOS (Automated Empirical Optimization of Software) paradigm, with the present emphasis on the Basic Linear Algebra Subprograms (BLAS), a widely used, performance-critical, linear algebra kernel library. *homepage*: http://math-atlas.sourceforge.net ========== ================= ================== version versionsuffix toolchain ========== ================= ================== ``3.10.2`` ``-LAPACK-3.6.1`` ``GCC/5.4.0-2.26`` ========== ================= ================== .. _list_software_atomate_747: *atomate* +++++++++ atomate has implementations of FireWorks workflows for Materials Science. *homepage*: https://pythonhosted.org/atomate/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.4.4`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== .. _list_software_AtomPAW_633: *AtomPAW* +++++++++ AtomPAW is a Projector-Augmented Wave Dataset Generator that can be used both as a standalone program and a library. *homepage*: http://users.wfu.edu/natalie/papers/pwpaw/man.html =========== =============== version toolchain =========== =============== ``4.1.0.5`` ``intel/2018b`` ``4.1.0.6`` ``intel/2018b`` =========== =============== .. _list_software_atools_658: *atools* ++++++++ Tools to make using job arrays a lot more convenient. *homepage*: https://github.com/gjbex/atools ========= ================== ================= version versionsuffix toolchain ========= ================== ================= ``1.4.2`` ``-Python-2.7.12`` ``intel/2016b`` ``1.4.6`` ``-Python-2.7.16`` ``GCCcore/8.3.0`` ========= ================== ================= .. _list_software_ATSAS_380: *ATSAS* +++++++ ATSAS is a program suite for small-angle scattering data analysis from biological macromolecules. *homepage*: http://www.embl-hamburg.de/ExternalInfo/Research/Sax/software.html =========== =============== ========== version versionsuffix toolchain =========== =============== ========== ``2.5.1-1`` ``.el6.x86_64`` ``system`` ``2.5.1-1`` ``.sl5.x86_64`` ``system`` ``2.7.1-1`` ``.el7.x86_64`` ``system`` =========== =============== ========== .. _list_software_attr_443: *attr* ++++++ Commands for Manipulating Filesystem Extended Attributes *homepage*: https://savannah.nongnu.org/projects/attr ========== ================= version toolchain ========== ================= ``2.4.47`` ``GCCcore/8.2.0`` ========== ================= .. _list_software_AUGUSTUS_641: *AUGUSTUS* ++++++++++ AUGUSTUS is a program that predicts genes in eukaryotic genomic sequences *homepage*: http://bioinf.uni-greifswald.de/augustus/ ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``3.2.3`` ``-Python-2.7.13`` ``intel/2017a`` ``3.3`` ``foss/2018a`` ``3.3.2`` ``intel/2019a`` ``3.3.2`` ``-Python-2.7.13`` ``intel/2017a`` ``3.3.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``3.3.2`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============================== .. _list_software_Autoconf_831: *Autoconf* ++++++++++ Autoconf is an extensible package of M4 macros that produce shell scripts to automatically configure software source code packages. These scripts can adapt the packages to many kinds of UNIX-like systems without manual user intervention. Autoconf creates a configuration script for a package from a template file that lists the operating system features that the package can use, in the form of M4 macro calls. *homepage*: http://www.gnu.org/software/autoconf/ ======== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain ======== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``2.68`` ``foss/2016b`` ``2.69`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ======== ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_Autoconf-archive_1614: *Autoconf-archive* ++++++++++++++++++ The GNU Autoconf Archive is a collection of more than 500 macros for GNU Autoconf that have been contributed as free software by friendly supporters of the cause from all over the Internet. Every single one of those macros can be re-used without imposing any restrictions whatsoever on the licensing of the generated configure script. In particular, it is possible to use all those macros in configure scripts that are meant for non-free software. This policy is unusual for a Free Software Foundation project. The FSF firmly believes that software ought to be free, and software licenses like the GPL are specifically designed to ensure that derivative work based on free software must be free as well. In case of Autoconf, however, an exception has been made, because Autoconf is at such a pivotal position in the software development tool chain that the benefits from having this tool available as widely as possible outweigh the disadvantage that some authors may choose to use it, too, for proprietary software. *homepage*: https://www.gnu.org/software/autoconf-archive ============== ==================== version toolchain ============== ==================== ``2019.01.06`` ``GCC/8.2.0-2.31.1`` ============== ==================== .. _list_software_AutoDock_794: *AutoDock* ++++++++++ AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. *homepage*: http://autodock.scripps.edu/ =========== ============= version toolchain =========== ============= ``4.2.5.1`` ``GCC/5.2.0`` =========== ============= .. _list_software_AutoDock_Vina_1287: *AutoDock_Vina* +++++++++++++++ AutoDock Vina is an open-source program for doing molecular docking. *homepage*: http://vina.scripps.edu/index.html ========= ============== ========== version versionsuffix toolchain ========= ============== ========== ``1.1.2`` ``_linux_x86`` ``system`` ========= ============== ========== .. _list_software_AutoGrid_799: *AutoGrid* ++++++++++ AutoDock is a suite of automated docking tools. It is designed to predict how small molecules, such as substrates or drug candidates, bind to a receptor of known 3D structure. *homepage*: http://autodock.scripps.edu/ =========== ============= version toolchain =========== ============= ``4.2.5.1`` ``GCC/5.2.0`` =========== ============= .. _list_software_Automake_823: *Automake* ++++++++++ Automake: GNU Standards-compliant Makefile generator *homepage*: https://www.gnu.org/software/automake/automake.html ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.11.3`` ``foss/2016b`` ``1.14`` ``GCC/4.8.2``, ``intel/2016a`` ``1.14.1`` ``GCC/4.8.2`` ``1.15`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.15.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` ``1.16.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_Autotools_970: *Autotools* +++++++++++ This bundle collect the standard GNU build tools: Autoconf, Automake and libtool *homepage*: http://autotools.io ============ ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain ============ ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``20150119`` ``GCC/4.9.2`` ``20150215`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``20170619`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` ``20180311`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` ============ ====================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_awscli_643: *awscli* ++++++++ Universal Command Line Environment for AWS *homepage*: https://pypi.python.org/pypi/awscli ============ ================== =============== version versionsuffix toolchain ============ ================== =============== ``1.11.1`` ``-Python-2.7.12`` ``intel/2016b`` ``1.11.56`` ``-Python-2.7.12`` ``foss/2016b`` ``1.16.290`` ``-Python-3.6.6`` ``foss/2018b`` ============ ================== =============== .. _list_software_letter_b: *B* --- :ref:`list_software_Bader_478` - :ref:`list_software_BAGEL_347` - :ref:`list_software_bam-readcount_1314` - :ref:`list_software_BAMM_285` - :ref:`list_software_BamM_349` - :ref:`list_software_BamTools_801` - :ref:`list_software_BamUtil_686` - :ref:`list_software_Bandage_674` - :ref:`list_software_barrnap_742` - :ref:`list_software_basemap_729` - :ref:`list_software_Bash_382` - :ref:`list_software_bat_311` - :ref:`list_software_BayesAss_795` - :ref:`list_software_BayeScan_774` - :ref:`list_software_BayeScEnv_864` - :ref:`list_software_BayesTraits_1131` - :ref:`list_software_Bazel_494` - :ref:`list_software_bbcp_407` - :ref:`list_software_bbFTP_430` - :ref:`list_software_BBMap_418` - :ref:`list_software_bc_197` - :ref:`list_software_BCALM_351` - :ref:`list_software_BCEL_278` - :ref:`list_software_BCFtools_764` - :ref:`list_software_bcgTree_700` - :ref:`list_software_bcl2fastq2_948` - :ref:`list_software_bcolz_538` - :ref:`list_software_BDBag_400` - :ref:`list_software_beagle-lib_964` - :ref:`list_software_Beast_495` - :ref:`list_software_BeautifulSoup_1352` - :ref:`list_software_BEDOPS_445` - :ref:`list_software_BEDTools_732` - :ref:`list_software_behave_619` - :ref:`list_software_BerkeleyGW_977` - :ref:`list_software_BFAST_368` - :ref:`list_software_BFC_203` - :ref:`list_software_bibtexparser_1291` - :ref:`list_software_binutils_874` - :ref:`list_software_Bio-DB-HTS_745` - :ref:`list_software_Bio-SamTools_1145` - :ref:`list_software_bioawk_637` - :ref:`list_software_biobambam2_972` - :ref:`list_software_biomart-perl_1230` - :ref:`list_software_BioPerl_685` - :ref:`list_software_Biopython_956` - :ref:`list_software_biscuit_755` - :ref:`list_software_Bismark_713` - :ref:`list_software_Bison_507` - :ref:`list_software_bitarray_862` - :ref:`list_software_BLACS_357` - :ref:`list_software_BLASR_372` - :ref:`list_software_blasr_libcpp_1261` - :ref:`list_software_BLAST_374` - :ref:`list_software_BLAST+_417` - :ref:`list_software_BLAT_291` - :ref:`list_software_Blender_700` - :ref:`list_software_BLIS_298` - :ref:`list_software_Blitz++_603` - :ref:`list_software_BlobTools_912` - :ref:`list_software_Blosc_499` - :ref:`list_software_bmtagger_841` - :ref:`list_software_bnpy_441` - :ref:`list_software_BOINC_363` - :ref:`list_software_bokeh_521` - :ref:`list_software_BoltzTraP_898` - :ref:`list_software_Bonmin_611` - :ref:`list_software_Bonnie++_689` - :ref:`list_software_Boost_519` - :ref:`list_software_Boost.Python_1207` - :ref:`list_software_Bottleneck_1035` - :ref:`list_software_Bowtie_618` - :ref:`list_software_Bowtie2_668` - :ref:`list_software_Bpipe_496` - :ref:`list_software_bpp-core_792` - :ref:`list_software_bpp-phyl_812` - :ref:`list_software_bpp-seq_696` - :ref:`list_software_BRAKER_439` - :ref:`list_software_BreakDancer_1074` - :ref:`list_software_breseq_642` - :ref:`list_software_bsddb3_562` - :ref:`list_software_buildenv_857` - :ref:`list_software_Bullet_616` - :ref:`list_software_BUSCO_380` - :ref:`list_software_BWA_218` - :ref:`list_software_bwa-meth_789` - :ref:`list_software_bwakit_642` - :ref:`list_software_bwidget_742` - :ref:`list_software_BWISE_378` - :ref:`list_software_bx-python_937` - :ref:`list_software_BXH_XCEDE_TOOLS_1178` - :ref:`list_software_byacc_514` - :ref:`list_software_bzip2_487` .. _list_software_Bader_478: *Bader* +++++++ A fast algorithm for doing Bader's analysis on a charge density grid. *homepage*: http://theory.cm.utexas.edu/henkelman/code/bader/ ======== =============== version toolchain ======== =============== ``1.02`` ``intel/2018a`` ``1.03`` ``intel/2018b`` ======== =============== .. _list_software_BAGEL_347: *BAGEL* +++++++ BAGEL (Brilliantly Advanced General Electronic-structure Library) is a parallel electronic-structure program. *homepage*: http://www.nubakery.org ========= =============== version toolchain ========= =============== ``1.1.1`` ``intel/2016b`` ========= =============== .. _list_software_bam-readcount_1314: *bam-readcount* +++++++++++++++ Count DNA sequence reads in BAM files *homepage*: https://github.com/genome/bam-readcount ========= ============== version toolchain ========= ============== ``0.8.0`` ``foss/2018b`` ========= ============== .. _list_software_BAMM_285: *BAMM* ++++++ BAMM is oriented entirely towards detecting and quantifying heterogeneity in evolutionary rates. It uses reversible jump Markov chain Monte Carlo to automatically explore a vast universe of candidate models of lineage diversification and trait evolution. *homepage*: http://bamm-project.org/ ========= ============== version toolchain ========= ============== ``2.5.0`` ``foss/2016b`` ========= ============== .. _list_software_BamM_349: *BamM* ++++++ BamM is a c library, wrapped in python, that parses BAM files *homepage*: http://ecogenomics.github.io/BamM/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.7.3`` ``-Python-2.7.12`` ``foss/2016b`` ``1.7.3`` ``-Python-2.7.14`` ``foss/2018a`` ========= ================== ============== .. _list_software_BamTools_801: *BamTools* ++++++++++ BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files. *homepage*: https://github.com/pezmaster31/bamtools ========= ================================================================================================================================================ version toolchain ========= ================================================================================================================================================ ``2.4.0`` ``foss/2016b`` ``2.4.1`` ``intel/2017a`` ``2.5.0`` ``foss/2016b``, ``intel/2017b`` ``2.5.1`` ``GCC/8.2.0-2.31.1``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b`` ========= ================================================================================================================================================ .. _list_software_BamUtil_686: *BamUtil* +++++++++ BamUtil is a repository that contains several programs that perform operations on SAM/BAM files. All of these programs are built into a single executable, bam. *homepage*: http://genome.sph.umich.edu/wiki/BamUtil ========== =============== version toolchain ========== =============== ``1.0.13`` ``intel/2016b`` ``1.0.14`` ``intel/2018a`` ========== =============== .. _list_software_Bandage_674: *Bandage* +++++++++ Bandage is a program for visualising de novo assembly graphs *homepage*: http://rrwick.github.io/Bandage/ ========= ============= ========== version versionsuffix toolchain ========= ============= ========== ``0.8.1`` ``_Centos`` ``system`` ``0.8.1`` ``_Ubuntu`` ``system`` ========= ============= ========== .. _list_software_barrnap_742: *barrnap* +++++++++ Barrnap (BAsic Rapid Ribosomal RNA Predictor) predicts the location of ribosomal RNA genes in genomes. *homepage*: https://github.com/tseemann/barrnap ======= ==================================== version toolchain ======= ==================================== ``0.9`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` ======= ==================================== .. _list_software_basemap_729: *basemap* +++++++++ The matplotlib basemap toolkit is a library for plotting 2D data on maps in Python *homepage*: http://matplotlib.org/basemap/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.0.7`` ``-Python-2.7.13`` ``intel/2017a`` ``1.0.7`` ``-Python-3.6.3`` ``intel/2017b`` ``1.0.7`` ``-Python-3.6.4`` ``intel/2018a`` ``1.2.0`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================== =============== .. _list_software_Bash_382: *Bash* ++++++ Bash is an sh-compatible command language interpreter that executes commands read from the standard input or from a file. Bash also incorporates useful features from the Korn and C shells (ksh and csh). *homepage*: http://www.gnu.org/software/bash ======= ============= version toolchain ======= ============= ``4.3`` ``GCC/4.9.2`` ======= ============= .. _list_software_bat_311: *bat* +++++ The BAT Python package supports the processing and analysis of Bro data with Pandas, scikit-learn, and Spark *homepage*: https://pypi.python.org/pypi/bat ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``0.3.3`` ``-Python-3.6.3`` ``intel/2017b`` ========= ================= =============== .. _list_software_BayesAss_795: *BayesAss* ++++++++++ BayesAss: Bayesian Inference of Recent Migration Using Multilocus Genotypes *homepage*: http://www.rannala.org/?page_id=245 ========= ============== version toolchain ========= ============== ``3.0.4`` ``foss/2016a`` ========= ============== .. _list_software_BayeScan_774: *BayeScan* ++++++++++ BayeScan aims at identifying candidate loci under natural selection from genetic data, using differences in allele frequencies between populations. *homepage*: http://cmpg.unibe.ch/software/BayeScan/ ======= =============================================== version toolchain ======= =============================================== ``2.1`` ``foss/2016a``, ``foss/2018a``, ``intel/2018a`` ======= =============================================== .. _list_software_BayeScEnv_864: *BayeScEnv* +++++++++++ BayeScEnv is a Fst-based, genome-scan method that uses environmental variables to detect local adaptation. *homepage*: https://github.com/devillemereuil/bayescenv ======= ============== version toolchain ======= ============== ``1.1`` ``foss/2016a`` ======= ============== .. _list_software_BayesTraits_1131: *BayesTraits* +++++++++++++ BayesTraits is a computer package for performing analyses of trait evolution among groups of species for which a phylogeny or sample of phylogenies is available. This new package incoporates our earlier and separate programes Multistate, Discrete and Continuous. BayesTraits can be applied to the analysis of traits that adopt a finite number of discrete states, or to the analysis of continuously varying traits. Hypotheses can be tested about models of evolution, about ancestral states and about correlations among pairs of traits. *homepage*: http://www.evolution.reading.ac.uk/BayesTraitsV1.html =============== ================= ========== version versionsuffix toolchain =============== ================= ========== ``1.0-linux32`` ``system`` ``2.0`` ``-Beta-Linux64`` ``system`` =============== ================= ========== .. _list_software_Bazel_494: *Bazel* +++++++ Bazel is a build tool that builds code quickly and reliably. It is used to build the majority of Google's software. *homepage*: https://bazel.io/ ========== ==================================== version toolchain ========== ==================================== ``0.4.4`` ``system`` ``0.7.0`` ``GCCcore/6.4.0`` ``0.10.0`` ``GCCcore/6.4.0`` ``0.11.0`` ``GCCcore/6.4.0`` ``0.11.1`` ``GCCcore/6.4.0`` ``0.12.0`` ``GCCcore/6.4.0`` ``0.16.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``0.18.0`` ``GCCcore/7.3.0`` ``0.20.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``0.25.2`` ``GCCcore/8.2.0`` ``0.26.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``0.29.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``1.1.0`` ``GCCcore/8.3.0`` ========== ==================================== .. _list_software_bbcp_407: *bbcp* ++++++ BBCP is an alternative to Gridftp when transferring large amounts of data, capable of breaking up your transfer into multiple simultaneous transferring streams, thereby transferring data much faster than single-streaming utilities such as SCP and SFTP. See details at http://pcbunn.cithep.caltech.edu/bbcp/using_bbcp.htm or http://www.nics.tennessee.edu/computing-resources/data-transfer/bbcp *homepage*: http://www.slac.stanford.edu/~abh/bbcp/ ================= ================== ========== version versionsuffix toolchain ================= ================== ========== ``12.01.30.00.0`` ``-amd64_linux26`` ``system`` ================= ================== ========== .. _list_software_bbFTP_430: *bbFTP* +++++++ bbFTP is a file transfer software. It implements its own transfer protocol, which is optimized for large files (larger than 2GB) and secure as it does not read the password in a file and encrypts the connection information. bbFTP main features are: * Encoded username and password at connection * SSH and Certificate authentication modules * Multi-stream transfer * Big windows as defined in RFC1323 * On-the-fly data compression * Automatic retry * Customizable time-outs * Transfer simulation * AFS authentication integration * RFIO interface *homepage*: http://doc.in2p3.fr/bbftp/ ========= =============== version toolchain ========= =============== ``3.2.1`` ``intel/2016a`` ========= =============== .. _list_software_BBMap_418: *BBMap* +++++++ BBMap short read aligner, and other bioinformatic tools. *homepage*: https://sourceforge.net/projects/bbmap/ ========== =================== =============================== version versionsuffix toolchain ========== =================== =============================== ``36.62`` ``-Java-1.8.0_112`` ``intel/2016b`` ``37.93`` ``foss/2018a``, ``intel/2018a`` ``38.26`` ``foss/2018b`` ``38.50b`` ``GCC/8.2.0-2.31.1`` ========== =================== =============================== .. _list_software_bc_197: *bc* ++++ bc is an arbitrary precision numeric processing language. *homepage*: https://www.gnu.org/software/bc/ =========== ============= version toolchain =========== ============= ``1.06.95`` ``GCC/4.8.2`` =========== ============= .. _list_software_BCALM_351: *BCALM* +++++++ de Bruijn graph compaction in low memory *homepage*: https://github.com/GATB/bcalm ========= ============== version toolchain ========= ============== ``2.2.0`` ``foss/2018a`` ========= ============== .. _list_software_BCEL_278: *BCEL* ++++++ The Byte Code Engineering Library (Apache Commons BCEL™) is intended to give users a convenient way to analyze, create, and manipulate (binary) Java class files (those ending with .class). *homepage*: http://commons.apache.org/proper/commons-bcel/ ======= ============= ========== version versionsuffix toolchain ======= ============= ========== ``5.2`` ``-Java-1.8`` ``system`` ======= ============= ========== .. _list_software_BCFtools_764: *BCFtools* ++++++++++ Samtools is a suite of programs for interacting with high-throughput sequencing data. BCFtools - Reading/writing BCF2/VCF/gVCF files and calling/filtering/summarising SNP and short indel sequence variants *homepage*: http://www.htslib.org/ ======= ========================================================================================= version toolchain ======= ========================================================================================= ``1.3`` ``foss/2016a``, ``intel/2016a`` ``1.6`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` ``1.9`` ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ======= ========================================================================================= .. _list_software_bcgTree_700: *bcgTree* +++++++++ Automatized phylogenetic tree building from bacterial core genomes. *homepage*: https://github.com/molbiodiv/bcgTree ========== ================ =============== version versionsuffix toolchain ========== ================ =============== ``1.0.10`` ``-Perl-5.26.1`` ``intel/2018a`` ========== ================ =============== .. _list_software_bcl2fastq2_948: *bcl2fastq2* ++++++++++++ bcl2fastq Conversion Software both demultiplexes data and converts BCL files generated by Illumina sequencing systems to standard FASTQ file formats for downstream analysis. *homepage*: https://support.illumina.com/sequencing/sequencing_software/bcl2fastq-conversion-software.html ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``2.19.1`` ``-Python-2.7.12`` ``foss/2016b`` ``2.20.0`` ``foss/2018b``, ``intel/2019a`` ``2.20.0`` ``-Python-2.7.12`` ``foss/2016b`` ``2.20.0`` ``-Python-2.7.14`` ``intel/2017b`` ========== ================== =============================== .. _list_software_bcolz_538: *bcolz* +++++++ bcolz provides columnar, chunked data containers that can be compressed either in-memory and on-disk. Column storage allows for efficiently querying tables, as well as for cheap column addition and removal. It is based on NumPy, and uses it as the standard data container to communicate with bcolz objects, but it also comes with support for import/export facilities to/from HDF5/PyTables tables and pandas dataframes. *homepage*: http://bcolz.blosc.org/en/latest/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.1.1`` ``-Python-2.7.13`` ``foss/2017a`` ========= ================== ============== .. _list_software_BDBag_400: *BDBag* +++++++ The bdbag utilities are a collection of software programs for working with BagIt packages that conform to the Bagit and Bagit/RO profiles. *homepage*: https://github.com/fair-research/bdbag ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.4.1`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============== .. _list_software_beagle-lib_964: *beagle-lib* ++++++++++++ beagle-lib is a high-performance library that can perform the core calculations at the heart of most Bayesian and Maximum Likelihood phylogenetics packages. *homepage*: https://github.com/beagle-dev/beagle-lib ========= ================ =============================== version versionsuffix toolchain ========= ================ =============================== ``2.1.2`` ``foss/2016a``, ``foss/2017a`` ``3.0.1`` ``foss/2018a``, ``intel/2018a`` ``3.0.2`` ``foss/2018b`` ``3.0.2`` ``-CUDA-9.2.88`` ``foss/2018b`` ``3.1.2`` ``GCC/8.2.0-2.31.1`` ========= ================ =============================== .. _list_software_Beast_495: *Beast* +++++++ BEAST is a cross-platform program for Bayesian MCMC analysis of molecular sequences. It is entirely orientated towards rooted, time-measured phylogenies inferred using strict or relaxed molecular clock models. It can be used as a method of reconstructing phylogenies but is also a framework for testing evolutionary hypotheses without conditioning on a single tree topology. BEAST uses MCMC to average over tree space, so that each tree is weighted proportional to its posterior probability. *homepage*: http://beast2.org/ ========== ==================== version toolchain ========== ==================== ``1.8.4`` ``system`` ``1.10.1`` ``intel/2018a`` ``1.10.4`` ``GCC/8.2.0-2.31.1`` ``2.4.0`` ``foss/2016a`` ``2.4.7`` ``foss/2017a`` ``2.5.0`` ``foss/2018a`` ``2.5.1`` ``foss/2018b`` ``2.5.2`` ``GCC/8.2.0-2.31.1`` ========== ==================== .. _list_software_BeautifulSoup_1352: *BeautifulSoup* +++++++++++++++ Beautiful Soup is a Python library designed for quick turnaround projects like screen-scraping. *homepage*: https://www.crummy.com/software/BeautifulSoup ========= ================= ================= version versionsuffix toolchain ========= ================= ================= ``4.6.0`` ``-Python-3.6.3`` ``intel/2017b`` ``4.6.3`` ``-Python-3.6.4`` ``intel/2018a`` ``4.7.1`` ``-Python-3.6.6`` ``intel/2018b`` ``4.8.0`` ``GCCcore/8.2.0`` ========= ================= ================= .. _list_software_BEDOPS_445: *BEDOPS* ++++++++ BEDOPS is an open-source command-line toolkit that performs highly efficient and scalable Boolean and other set operations, statistical calculations, archiving, conversion and other management of genomic data of arbitrary scale. Tasks can be easily split by chromosome for distributing whole-genome analyses across a computational cluster. *homepage*: http://bedops.readthedocs.io/en/latest/index.html ========== =============================== version toolchain ========== =============================== ``2.4.1`` ``GCC/4.8.4`` ``2.4.2`` ``GCC/4.8.2`` ``2.4.20`` ``system`` ``2.4.26`` ``system`` ``2.4.30`` ``foss/2016b`` ``2.4.32`` ``foss/2018a``, ``intel/2018a`` ``2.4.35`` ``foss/2018b`` ========== =============================== .. _list_software_BEDTools_732: *BEDTools* ++++++++++ The BEDTools utilities allow one to address common genomics tasks such as finding feature overlaps and computing coverage. The utilities are largely based on four widely-used file formats: BED, GFF/GTF, VCF, and SAM/BAM. *homepage*: https://github.com/arq5x/bedtools2 ========== ==================================================================================== version toolchain ========== ==================================================================================== ``2.25.0`` ``foss/2016a`` ``2.26.0`` ``GCCcore/6.4.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``2.27.1`` ``GCCcore/6.4.0``, ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` ``2.28.0`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ========== ==================================================================================== .. _list_software_behave_619: *behave* ++++++++ behave: Behavior-driven development (or BDD) is an agile software development technique that encourages collaboration between developers, QA and non-technical or business participants in a software project. *homepage*: http://pythonhosted.org/behave ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.2.5`` ``-Python-2.7.12`` ``foss/2016b`` ``1.2.6`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================== =============== .. _list_software_BerkeleyGW_977: *BerkeleyGW* ++++++++++++ The BerkeleyGW Package is a set of computer codes that calculates the quasiparticle properties and the optical responses of a large variety of materials from bulk periodic crystals to nanostructures such as slabs, wires and molecules. *homepage*: http://www.berkeleygw.org ============= ================================================================ version toolchain ============= ================================================================ ``1.0.6`` ``intel/2016.02-GCC-4.9`` ``1.1-beta2`` ``intel/2016.02-GCC-4.9`` ``1.2.0`` ``intel/2017a``, ``intel/2018a`` ``2.0.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ============= ================================================================ .. _list_software_BFAST_368: *BFAST* +++++++ BFAST facilitates the fast and accurate mapping of short reads to reference sequences. Some advantages of BFAST include: 1) Speed: enables billions of short reads to be mapped quickly. 2) Accuracy: A priori probabilities for mapping reads with defined set of variants. 3) An easy way to measurably tune accuracy at the expense of speed. *homepage*: http://bfast.sourceforge.net/ ========== ============== version toolchain ========== ============== ``0.7.0a`` ``foss/2016b`` ========== ============== .. _list_software_BFC_203: *BFC* +++++ BFC is a standalone high-performance tool for correcting sequencing errors from Illumina sequencing data. It is specifically designed for high-coverage whole-genome human data, though also performs well for small genomes. *homepage*: https://github.com/lh3/bfc ======= ============== version toolchain ======= ============== ``1`` ``foss/2018a`` ======= ============== .. _list_software_bibtexparser_1291: *bibtexparser* ++++++++++++++ Bibtex parser in Python 2.7 and 3.x *homepage*: https://github.com/sciunto-org/python-bibtexparser ========= ================= version toolchain ========= ================= ``1.1.0`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_binutils_874: *binutils* ++++++++++ binutils: GNU binary utilities *homepage*: https://directory.fsf.org/project/binutils/ ========== ======================================================================================================================================================================================== version toolchain ========== ======================================================================================================================================================================================== ``2.25`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``system`` ``2.25.1`` ``system`` ``2.26`` ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``system`` ``2.27`` ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``system`` ``2.28`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``system`` ``2.29`` ``GCCcore/7.2.0``, ``GCCcore/system``, ``system`` ``2.30`` ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``system`` ``2.31.1`` ``GCCcore/7.4.0``, ``GCCcore/8.2.0``, ``system`` ``2.32`` ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` ========== ======================================================================================================================================================================================== .. _list_software_Bio-DB-HTS_745: *Bio-DB-HTS* ++++++++++++ Read files using HTSlib including BAM/CRAM, Tabix and BCF database files *homepage*: https://metacpan.org/release/Bio-DB-HTS ======== ================ =============================== version versionsuffix toolchain ======== ================ =============================== ``2.11`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``2.11`` ``-Perl-5.26.1`` ``intel/2018a`` ``2.11`` ``-Perl-5.28.0`` ``foss/2018b`` ``3.01`` ``-Perl-5.28.1`` ``GCC/8.2.0-2.31.1`` ======== ================ =============================== .. _list_software_Bio-SamTools_1145: *Bio-SamTools* ++++++++++++++ This is a Perl interface to the SAMtools sequence alignment interface. *homepage*: http://search.cpan.org/~lds/Bio-SamTools/ ======== ================ =============== version versionsuffix toolchain ======== ================ =============== ``1.43`` ``-Perl-5.24.1`` ``intel/2017a`` ======== ================ =============== .. _list_software_bioawk_637: *bioawk* ++++++++ Bioawk is an extension to Brian Kernighan's awk, adding the support of several common biological data formats, including optionally gzip'ed BED, GFF, SAM, VCF, FASTA/Q and TAB-delimited formats with column names. *homepage*: https://github.com/lh3/bioawk ======= ============== version toolchain ======= ============== ``1.0`` ``foss/2018b`` ======= ============== .. _list_software_biobambam2_972: *biobambam2* ++++++++++++ Tools for processing BAM files *homepage*: https://github.com/gt1/biobambam2 ========== =============== version toolchain ========== =============== ``2.0.87`` ``intel/2018a`` ========== =============== .. _list_software_biomart-perl_1230: *biomart-perl* ++++++++++++++ The BioMart Perl API allows you to go a step further with BioMart and integrate BioMart Perl Code into custom Perl scripts. *homepage*: https://useast.ensembl.org/info/data/biomart/biomart_perl_api.html =============== ================ ================= version versionsuffix toolchain =============== ================ ================= ``0.7_e6db561`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` =============== ================ ================= .. _list_software_BioPerl_685: *BioPerl* +++++++++ Bioperl is the product of a community effort to produce Perl code which is useful in biology. Examples include Sequence objects, Alignment objects and database searching objects. *homepage*: http://www.bioperl.org/ =========== ================ =============================== version versionsuffix toolchain =========== ================ =============================== ``1.6.924`` ``-Perl-5.20.3`` ``intel/2016a`` ``1.6.924`` ``-Perl-5.22.1`` ``foss/2016a`` ``1.7.0`` ``-Perl-5.24.0`` ``foss/2016b`` ``1.7.1`` ``-Perl-5.24.0`` ``intel/2016b`` ``1.7.1`` ``-Perl-5.24.1`` ``intel/2017a`` ``1.7.2`` ``GCCcore/8.3.0`` ``1.7.2`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``1.7.2`` ``-Perl-5.26.1`` ``intel/2018a`` ``1.7.2`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` ``1.7.2`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` =========== ================ =============================== .. _list_software_Biopython_956: *Biopython* +++++++++++ Biopython is a set of freely available tools for biological computation written in Python by an international team of developers. It is a distributed collaborative effort to develop Python libraries and applications which address the needs of current and future work in bioinformatics. *homepage*: https://www.biopython.org ======== ================== =================================================== version versionsuffix toolchain ======== ================== =================================================== ``1.65`` ``-Python-2.7.11`` ``foss/2016a`` ``1.68`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``1.68`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` ``1.70`` ``-Python-2.7.13`` ``foss/2017a`` ``1.70`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.70`` ``-Python-3.6.1`` ``intel/2017a`` ``1.70`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.71`` ``-Python-2.7.14`` ``intel/2018a`` ``1.71`` ``-Python-3.6.4`` ``foss/2018a`` ``1.72`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``1.72`` ``-Python-3.6.6`` ``foss/2018b`` ``1.73`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``1.73`` ``-Python-3.6.6`` ``foss/2018b`` ``1.74`` ``foss/2019a`` ``1.75`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ======== ================== =================================================== .. _list_software_biscuit_755: *biscuit* +++++++++ Utilities to help analyze bisulfite-treated sequence data *homepage*: https://github.com/zwdzwd/biscuit ========= ============== version toolchain ========= ============== ``0.1.4`` ``foss/2016a`` ========= ============== .. _list_software_Bismark_713: *Bismark* +++++++++ A tool to map bisulfite converted sequence reads and determine cytosine methylation states *homepage*: http://www.bioinformatics.babraham.ac.uk/projects/bismark/ ========== =============================== version toolchain ========== =============================== ``0.19.0`` ``intel/2017b`` ``0.20.1`` ``foss/2018b``, ``intel/2018b`` ========== =============================== .. _list_software_Bison_507: *Bison* +++++++ Bison is a general-purpose parser generator that converts an annotated context-free grammar into a deterministic LR or generalized LR (GLR) parser employing LALR(1) parser tables. *homepage*: http://www.gnu.org/software/bison ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``2.7`` ``GCC/4.8.1``, ``GCC/4.8.4``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``system`` ``3.0.2`` ``GCC/4.8.2`` ``3.0.3`` ``GCC/4.9.2`` ``3.0.4`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``GCCcore/system``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``3.0.5`` ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/system``, ``system`` ``3.2.2`` ``GCCcore/7.4.0`` ``3.3.2`` ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``system`` ========= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_bitarray_862: *bitarray* ++++++++++ bitarray provides an object type which efficiently represents an array of booleans *homepage*: https://github.com/ilanschnell/bitarray ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.8.3`` ``-Python-2.7.15`` ``intel/2018b`` ``0.8.3`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================== =============== .. _list_software_BLACS_357: *BLACS* +++++++ The BLACS (Basic Linear Algebra Communication Subprograms) project is an ongoing investigation whose purpose is to create a linear algebra oriented message passing interface that may be implemented efficiently and uniformly across a large range of distributed memory platforms. *homepage*: http://www.netlib.org/blacs/ ======= =================== version toolchain ======= =================== ``1.1`` ``gmvapich2/2016a`` ======= =================== .. _list_software_BLASR_372: *BLASR* +++++++ The PacBio® long read aligner *homepage*: https://github.com/PacificBiosciences/blasr ============ =============== version toolchain ============ =============== ``2.2`` ``intel/2016b`` ``5.3.3`` ``gompi/2019a`` ``20170330`` ``intel/2017a`` ============ =============== .. _list_software_blasr_libcpp_1261: *blasr_libcpp* ++++++++++++++ Blasr_libcpp is a library used by blasr and other executables such as samtoh5, loadPulses for analyzing PacBio sequences *homepage*: https://github.com/PacificBiosciences/blasr_libcpp ============ =============== version toolchain ============ =============== ``20170426`` ``intel/2017a`` ============ =============== .. _list_software_BLAST_374: *BLAST* +++++++ Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. *homepage*: http://blast.ncbi.nlm.nih.gov/ ========== ================= ========== version versionsuffix toolchain ========== ================= ========== ``2.2.26`` ``-Linux_x86_64`` ``system`` ``2.8.1`` ``-Linux_x86_64`` ``system`` ========== ================= ========== .. _list_software_BLAST+_417: *BLAST+* ++++++++ Basic Local Alignment Search Tool, or BLAST, is an algorithm for comparing primary biological sequence information, such as the amino-acid sequences of different proteins or the nucleotides of DNA sequences. *homepage*: http://blast.ncbi.nlm.nih.gov/ ========== ================== ================================================================ version versionsuffix toolchain ========== ================== ================================================================ ``2.2.31`` ``system`` ``2.3.0`` ``-Python-2.7.11`` ``foss/2016a`` ``2.6.0`` ``-Python-2.7.12`` ``foss/2016b`` ``2.6.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` ``2.6.0`` ``-Python-2.7.14`` ``intel/2017b`` ``2.7.1`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` ``2.7.1`` ``-Python-2.7.14`` ``intel/2017b`` ``2.8.1`` ``foss/2018b`` ``2.9.0`` ``gompi/2019a``, ``gompi/2019b``, ``iimpi/2019a`` ========== ================== ================================================================ .. _list_software_BLAT_291: *BLAT* ++++++ BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 25 bases or more. *homepage*: http://genome.ucsc.edu/FAQ/FAQblat.html ======= ====================================================================================== version toolchain ======= ====================================================================================== ``3.5`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018b``, ``intel/2016b``, ``intel/2017a`` ======= ====================================================================================== .. _list_software_Blender_700: *Blender* +++++++++ Blender is the free and open source 3D creation suite. It supports the entirety of the 3D pipeline-modeling, rigging, animation, simulation, rendering, compositing and motion tracking, even video editing and game creation. *homepage*: https://www.blender.org/ ========= ============================= =============================== version versionsuffix toolchain ========= ============================= =============================== ``2.77a`` ``-Python-3.5.2`` ``intel/2016b`` ``2.79`` ``-Python-3.6.1`` ``intel/2017a`` ``2.79b`` ``-Python-3.6.6`` ``intel/2018b`` ``2.79b`` ``-Python-3.6.6-CUDA-9.2.88`` ``foss/2018b`` ``2.81`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========= ============================= =============================== .. _list_software_BLIS_298: *BLIS* ++++++ AMD fork of BLIS. BLIS is a portable software framework for instantiating high-performance BLAS-like dense linear algebra libraries. *homepage*: https://developer.amd.com/amd-cpu-libraries/blas-library/ ========= ============= ================== version versionsuffix toolchain ========= ============= ================== ``0.3.2`` ``GCC/7.3.0-2.30`` ``0.6.0`` ``GCC/8.3.0-2.32`` ``1.2`` ``-amd`` ``GCC/7.3.0-2.30`` ========= ============= ================== .. _list_software_Blitz++_603: *Blitz++* +++++++++ Blitz++ is a (LGPLv3+) licensed meta-template library for array manipulation in C++ with a speed comparable to Fortran implementations, while preserving an object-oriented interface *homepage*: http://blitz.sourceforge.net/ ======== ================================= version toolchain ======== ================================= ``0.10`` ``GCCcore/6.4.0``, ``foss/2016a`` ======== ================================= .. _list_software_BlobTools_912: *BlobTools* +++++++++++ A modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets. *homepage*: https://blobtools.readme.io/docs ============ ================== ============== version versionsuffix toolchain ============ ================== ============== ``20180528`` ``-Python-2.7.15`` ``foss/2018b`` ============ ================== ============== .. _list_software_Blosc_499: *Blosc* +++++++ Blosc, an extremely fast, multi-threaded, meta-compressor library *homepage*: http://www.blosc.org/ ========== ================================================================== version toolchain ========== ================================================================== ``1.11.1`` ``intel/2016b`` ``1.12.1`` ``GCCcore/6.4.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2017a`` ``1.14.2`` ``GCCcore/6.4.0``, ``foss/2016a`` ``1.14.4`` ``GCCcore/7.3.0`` ``1.17.0`` ``GCCcore/8.2.0`` ========== ================================================================== .. _list_software_bmtagger_841: *bmtagger* ++++++++++ Best Match Tagger for removing human reads from metagenomics datasets *homepage*: ftp://ftp.ncbi.nlm.nih.gov/pub/agarwala/bmtagger/ ========= =============================== version toolchain ========= =============================== ``3.101`` ``foss/2018b``, ``gompi/2019a`` ========= =============================== .. _list_software_bnpy_441: *bnpy* ++++++ Bayesian nonparametric machine learning for python provides code for training popular clustering models on large datasets. The focus is on Bayesian nonparametric models based on the Dirichlet process, but it also provides parametric counterparts. *homepage*: https://github.com/bnpy/bnpy ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``0.1.6`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== ============== .. _list_software_BOINC_363: *BOINC* +++++++ BOINC is a program that lets you donate your idle computer time to science projects like SETI@home, Climateprediction.net, Rosetta@home, World Community Grid, and many others. *homepage*: https://boinc.berkeley.edu ========== ============= ============= version versionsuffix toolchain ========== ============= ============= ``7.2.42`` ``-client`` ``GCC/4.8.2`` ========== ============= ============= .. _list_software_bokeh_521: *bokeh* +++++++ Statistical and novel interactive HTML plots for Python *homepage*: https://github.com/bokeh/bokeh =========== ================== =============================== version versionsuffix toolchain =========== ================== =============================== ``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` ``0.12.3`` ``-Python-3.5.2`` ``intel/2016b`` ``0.12.15`` ``-Python-3.6.4`` ``intel/2018a`` ``1.0.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.3.4`` ``-Python-3.7.2`` ``foss/2019a`` ``1.4.0`` ``-Python-3.7.4`` ``foss/2019b`` =========== ================== =============================== .. _list_software_BoltzTraP_898: *BoltzTraP* +++++++++++ Boltzmann Transport Properties (BoltzTraP) is a program for calculating the semi-classic transport coefficients. *homepage*: http://www.icams.de/content/departments/cmat/boltztrap/ ========= =============== version toolchain ========= =============== ``1.2.5`` ``intel/2016a`` ========= =============== .. _list_software_Bonmin_611: *Bonmin* ++++++++ Ipopt (Interior Point OPTimizer, pronounced eye-pea-Opt) is a software package for large-scale nonlinear optimization. *homepage*: https://coin-or.github.io/Ipopt ========= =============== version toolchain ========= =============== ``1.8.7`` ``intel/2019a`` ========= =============== .. _list_software_Bonnie++_689: *Bonnie++* ++++++++++ Bonnie++-1.97: Enhanced performance Test of Filesystem I/O *homepage*: http://www.coker.com.au/bonnie++/ ======== ============== version toolchain ======== ============== ``1.97`` ``foss/2016a`` ======== ============== .. _list_software_Boost_519: *Boost* +++++++ Boost provides free peer-reviewed portable C++ source libraries. *homepage*: https://www.boost.org/ ========== ================== ==================================================================== version versionsuffix toolchain ========== ================== ==================================================================== ``1.54.0`` ``-Python-2.7.12`` ``foss/2016b`` ``1.55.0`` ``system`` ``1.55.0`` ``-Python-2.7.11`` ``foss/2016a`` ``1.57.0`` ``-Python-2.7.10`` ``gimkl/2.11.5`` ``1.58.0`` ``intel/2017a`` ``1.58.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``1.58.0`` ``-serial`` ``GCC/4.9.2`` ``1.59.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``1.60.0`` ``foss/2016a``, ``intel/2016a`` ``1.60.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``1.60.0`` ``-Python-3.5.1`` ``foss/2016a`` ``1.61.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.61.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``1.61.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``1.61.0`` ``-Python-3.5.1`` ``foss/2016a`` ``1.62.0`` ``-Python-2.7.12`` ``intel/2016b`` ``1.63.0`` ``foss/2017a`` ``1.63.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``1.63.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` ``1.63.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` ``1.63.0`` ``-Python-3.5.2`` ``foss/2016b`` ``1.64.0`` ``gompi/2019a``, ``gompic/2019a``, ``intel/2017a`` ``1.64.0`` ``-Python-2.7.13`` ``intel/2017a`` ``1.65.0`` ``-Python-2.7.13`` ``intel/2017a`` ``1.65.1`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``1.65.1`` ``-Python-2.7.13`` ``intel/2017a`` ``1.65.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.65.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.66.0`` ``foss/2018a``, ``intel/2017b``, ``intel/2018.01``, ``intel/2018a`` ``1.66.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``1.66.0`` ``-Python-3.6.3`` ``intel/2018.01`` ``1.66.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.66.0`` ``-no_mpi`` ``GCCcore/6.4.0`` ``1.67.0`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` ``1.67.0`` ``-Python-2.7.14`` ``foss/2018a`` ``1.68.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``1.68.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.69.0`` ``intel/2019.01`` ``1.70.0`` ``gompi/2019a``, ``iimpi/2019a``, ``iimpic/2019a`` ``1.71.0`` ``gompi/2019b``, ``iimpi/2019b`` ========== ================== ==================================================================== .. _list_software_Boost.Python_1207: *Boost.Python* ++++++++++++++ Boost.Python is a C++ library which enables seamless interoperability between C++ and the Python programming language. *homepage*: https://boostorg.github.io/python ========== ================== =================================================== version versionsuffix toolchain ========== ================== =================================================== ``1.64.0`` ``gompi/2019a``, ``gompic/2019a`` ``1.65.1`` ``-Python-2.7.14`` ``intel/2017b`` ``1.66.0`` ``-Python-2.7.14`` ``intel/2018a`` ``1.66.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.67.0`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``1.67.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.70.0`` ``gompi/2019a``, ``iimpi/2019a`` ``1.71.0`` ``gompi/2019b`` ========== ================== =================================================== .. _list_software_Bottleneck_1035: *Bottleneck* ++++++++++++ Fast NumPy array functions written in C *homepage*: https://kwgoodman.github.io/bottleneck-doc ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``1.2.1`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== .. _list_software_Bowtie_618: *Bowtie* ++++++++ Bowtie is an ultrafast, memory-efficient short read aligner. It aligns short DNA sequences (reads) to the human genome. *homepage*: http://bowtie-bio.sourceforge.net/index.shtml =========== ======================================================================================================= version toolchain =========== ======================================================================================================= ``1.1.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a`` ``1.2.1.1`` ``foss/2016b``, ``intel/2017b`` ``1.2.2`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ``1.2.3`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` =========== ======================================================================================================= .. _list_software_Bowtie2_668: *Bowtie2* +++++++++ Bowtie 2 is an ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences. It is particularly good at aligning reads of about 50 up to 100s or 1,000s of characters, and particularly good at aligning to relatively long (e.g. mammalian) genomes. Bowtie 2 indexes the genome with an FM Index to keep its memory footprint small: for the human genome, its memory footprint is typically around 3.2 GB. Bowtie 2 supports gapped, local, and paired-end alignment modes. *homepage*: http://bowtie-bio.sourceforge.net/bowtie2/index.shtml =========== ============================================================== version toolchain =========== ============================================================== ``2.2.8`` ``foss/2016a`` ``2.2.9`` ``foss/2016a``, ``intel/2016b`` ``2.3.2`` ``foss/2016b``, ``foss/2017a``, ``intel/2017a`` ``2.3.3.1`` ``intel/2017b`` ``2.3.4`` ``intel/2017b`` ``2.3.4.1`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``2.3.4.2`` ``foss/2018b``, ``intel/2018b`` ``2.3.4.3`` ``foss/2017b`` ``2.3.5.1`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` =========== ============================================================== .. _list_software_Bpipe_496: *Bpipe* +++++++ Bpipe - a tool for running and managing bioinformatics pipelines *homepage*: http://docs.bpipe.org/ =========== =============== version toolchain =========== =============== ``0.9.9.2`` ``intel/2017a`` =========== =============== .. _list_software_bpp-core_792: *bpp-core* ++++++++++ Bio++ Core Library *homepage*: https://github.com/BioPP/bpp-core ========= ==================== version toolchain ========= ==================== ``2.4.1`` ``GCC/8.2.0-2.31.1`` ========= ==================== .. _list_software_bpp-phyl_812: *bpp-phyl* ++++++++++ Bio++ Phylogenetic Library *homepage*: https://github.com/BioPP/bpp-phyl ========= ==================== version toolchain ========= ==================== ``2.4.1`` ``GCC/8.2.0-2.31.1`` ========= ==================== .. _list_software_bpp-seq_696: *bpp-seq* +++++++++ Bio++ Sequence Library *homepage*: https://github.com/BioPP/bpp-seq ========= ==================== version toolchain ========= ==================== ``2.4.1`` ``GCC/8.2.0-2.31.1`` ========= ==================== .. _list_software_BRAKER_439: *BRAKER* ++++++++ BRAKER is a pipeline for fully automated prediction of protein coding genes with GeneMark-ES/ET and AUGUSTUS in novel eukaryotic genomes. *homepage*: https://github.com/Gaius-Augustus/BRAKER ========= =============== version toolchain ========= =============== ``2.1.2`` ``intel/2019a`` ========= =============== .. _list_software_BreakDancer_1074: *BreakDancer* +++++++++++++ BreakDancer is a Perl/C++ package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads *homepage*: http://gmt.genome.wustl.edu/packages/breakdancer ========= =============== version toolchain ========= =============== ``1.4.5`` ``intel/2017a`` ========= =============== .. _list_software_breseq_642: *breseq* ++++++++ breseq is a computational pipeline for the analysis of short-read re-sequencing data *homepage*: https://barricklab.org/breseq ========== ============= =============== version versionsuffix toolchain ========== ============= =============== ``0.35.0`` ``-R-3.6.0`` ``intel/2019a`` ========== ============= =============== .. _list_software_bsddb3_562: *bsddb3* ++++++++ bsddb3 is a nearly complete Python binding of the Oracle/Sleepycat C API for the Database Environment, Database, Cursor, Log Cursor, Sequence and Transaction objects. *homepage*: https://pypi.org/project/bsddb3/ ========= ================== ================== version versionsuffix toolchain ========= ================== ================== ``6.2.6`` ``GCCcore/8.2.0`` ``6.2.6`` ``-Python-2.7.15`` ``fosscuda/2018b`` ========= ================== ================== .. _list_software_buildenv_857: *buildenv* ++++++++++ This module sets a group of environment variables for compilers, linkers, maths libraries, etc., that you can use to easily transition between toolchains when building your software. To query the variables being set please use: module show *homepage*: None =========== ================================================================================================= version toolchain =========== ================================================================================================= ``default`` ``foss/2017b``, ``foss/2018b``, ``foss/2019b``, ``intel/2016b``, ``intel/2017a``, ``intel/2019b`` =========== ================================================================================================= .. _list_software_Bullet_616: *Bullet* ++++++++ Bullet professional 3D Game Multiphysics Library provides state of the art collision detection, soft body and rigid body dynamics. *homepage*: http://bulletphysics.org/ ========== =============================== version toolchain ========== =============================== ``2.83.7`` ``foss/2016a``, ``intel/2016a`` ========== =============================== .. _list_software_BUSCO_380: *BUSCO* +++++++ BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs *homepage*: http://busco.ezlab.org/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.22`` ``-Python-2.7.13`` ``intel/2017a`` ``2.0.1`` ``-Python-2.7.13`` ``intel/2017a`` ``3.0.2`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============== .. _list_software_BWA_218: *BWA* +++++ Burrows-Wheeler Aligner (BWA) is an efficient program that aligns relatively short nucleotide sequences against a long reference sequence such as the human genome. *homepage*: http://bio-bwa.sourceforge.net/ =========== ================================================================================================================================================================= version toolchain =========== ================================================================================================================================================================= ``0.7.12`` ``foss/2016b`` ``0.7.13`` ``foss/2016a``, ``intel/2016a`` ``0.7.15`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` ``0.7.16a`` ``foss/2016b``, ``intel/2017a`` ``0.7.17`` ``GCC/8.2.0-2.31.1``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` =========== ================================================================================================================================================================= .. _list_software_bwa-meth_789: *bwa-meth* ++++++++++ Fast and accurante alignment of BS-Seq reads. *homepage*: https://github.com/brentp/bwa-meth ========= ======================================== version toolchain ========= ======================================== ``0.2.2`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ========= ======================================== .. _list_software_bwakit_642: *bwakit* ++++++++ Bwakit is a self-consistent installation-free package of scripts and precompiled binaries, providing an end-to-end solution to read mapping. *homepage*: https://github.com/lh3/bwa/tree/master/bwakit ========== ============== ========== version versionsuffix toolchain ========== ============== ========== ``0.7.15`` ``_x64-linux`` ``system`` ========== ============== ========== .. _list_software_bwidget_742: *bwidget* +++++++++ The BWidget Toolkit is a high-level Widget Set for Tcl/Tk built using native Tcl/Tk 8.x namespaces. *homepage*: https://core.tcl-lang.org/bwidget/home ========== ================= version toolchain ========== ================= ``1.9.13`` ``GCCcore/8.2.0`` ========== ================= .. _list_software_BWISE_378: *BWISE* +++++++ de Bruijn Workflow using Integral information of Short pair End reads *homepage*: https://github.com/Malfoy/BWISE ============ ================= ============== version versionsuffix toolchain ============ ================= ============== ``20180820`` ``-Python-3.6.4`` ``foss/2018a`` ============ ================= ============== .. _list_software_bx-python_937: *bx-python* +++++++++++ The bx-python project is a Python library and associated set of scripts to allow for rapid implementation of genome scale analyses. *homepage*: https://github.com/bxlab/bx-python ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.7.4`` ``-Python-2.7.12`` ``foss/2016b`` ``0.7.4`` ``-Python-2.7.13`` ``intel/2017a`` ``0.8.1`` ``-Python-2.7.14`` ``intel/2018a`` ``0.8.2`` ``-Python-3.6.6`` ``foss/2018b`` ``0.8.4`` ``foss/2019a`` ========= ================== =============== .. _list_software_BXH_XCEDE_TOOLS_1178: *BXH_XCEDE_TOOLS* +++++++++++++++++ A collection of data processing and image analysis tools for data in BXH or XCEDE format. This includes data format encapsulation/conversion, event-related analysis, QA tools, and more. These tools form the basis of the fBIRN QA procedures and are also distributed as part of the fBIRN Data Upload Scripts. *homepage*: http://www.nitrc.org/projects/bxh_xcede_tools/ ========== ========== version toolchain ========== ========== ``1.11.1`` ``system`` ========== ========== .. _list_software_byacc_514: *byacc* +++++++ Berkeley Yacc (byacc) is generally conceded to be the best yacc variant available. In contrast to bison, it is written to avoid dependencies upon a particular compiler. *homepage*: http://invisible-island.net/byacc/byacc.html ============ =============================== version toolchain ============ =============================== ``20160324`` ``intel/2016a`` ``20160606`` ``foss/2016b``, ``intel/2016b`` ``20170709`` ``GCCcore/6.4.0`` ============ =============================== .. _list_software_bzip2_487: *bzip2* +++++++ bzip2 is a freely available, patent free, high-quality data compressor. It typically compresses files to within 10% to 15% of the best available techniques (the PPM family of statistical compressors), whilst being around twice as fast at compression and six times faster at decompression. *homepage*: https://sourceware.org/bzip2 ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.0.6`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.0.8`` ``GCCcore/8.3.0`` ========= ============================================================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_letter_c: *C* --- :ref:`list_software_C3D_186` - :ref:`list_software_cadaver_726` - :ref:`list_software_Caffe_469` - :ref:`list_software_cairo_526` - :ref:`list_software_cairomm_744` - :ref:`list_software_Calendrical_1106` - :ref:`list_software_Cantera_702` - :ref:`list_software_canu_423` - :ref:`list_software_Canvas_604` - :ref:`list_software_CAP3_263` - :ref:`list_software_CapnProto_918` - :ref:`list_software_Cargo_492` - :ref:`list_software_CastXML_636` - :ref:`list_software_Catch2_533` - :ref:`list_software_CatMAP_502` - :ref:`list_software_causalml_850` - :ref:`list_software_CaVEMan_603` - :ref:`list_software_CBLAS_357` - :ref:`list_software_ccache_599` - :ref:`list_software_CCL_210` - :ref:`list_software_cclib_509` - :ref:`list_software_CD-HIT_409` - :ref:`list_software_cDNA_Cupcake_1105` - :ref:`list_software_CDO_214` - :ref:`list_software_cdsapi_628` - :ref:`list_software_CellMix_686` - :ref:`list_software_CellRanger_991` - :ref:`list_software_Centrifuge_1036` - :ref:`list_software_CESM-deps_769` - :ref:`list_software_CFITSIO_529` - :ref:`list_software_cftime_632` - :ref:`list_software_CGAL_279` - :ref:`list_software_cget_419` - :ref:`list_software_CGNS_299` - :ref:`list_software_CharLS_541` - :ref:`list_software_charmm_632` - :ref:`list_software_CHARMM_440` - :ref:`list_software_CHASE_356` - :ref:`list_software_CheckM_555` - :ref:`list_software_Cheetah_690` - :ref:`list_software_CheMPS2_562` - :ref:`list_software_Chimera_697` - :ref:`list_software_ChimPipe_783` - :ref:`list_software_Chromaprint_1159` - :ref:`list_software_CIRCexplorer_1170` - :ref:`list_software_CIRCexplorer2_1220` - :ref:`list_software_Circos_611` - :ref:`list_software_CIRI_295` - :ref:`list_software_cisTEM_549` - :ref:`list_software_CITE-seq-Count_1233` - :ref:`list_software_Clang_485` - :ref:`list_software_Clang-Python-bindings_2063` - :ref:`list_software_CLAPACK_495` - :ref:`list_software_CLHEP_364` - :ref:`list_software_CLISP_379` - :ref:`list_software_ClonalFrameML_1245` - :ref:`list_software_CLooG_436` - :ref:`list_software_Clustal-Omega_1262` - :ref:`list_software_ClustalW2_865` - :ref:`list_software_Cluster-Buster_1412` - :ref:`list_software_ClusterShell_1242` - :ref:`list_software_CMake_449` - :ref:`list_software_CNT-ILP_503` - :ref:`list_software_CNVkit_559` - :ref:`list_software_CNVnator_779` - :ref:`list_software_CODEX2_421` - :ref:`list_software_Commet_613` - :ref:`list_software_Con3F_409` - :ref:`list_software_CONCOCT_521` - :ref:`list_software_configparser_1283` - :ref:`list_software_configurable-http-proxy_2381` - :ref:`list_software_ConnectomeWorkbench_1966` - :ref:`list_software_Control-FREEC_1139` - :ref:`list_software_CoordgenLibs_1211` - :ref:`list_software_Coot_405` - :ref:`list_software_core-counter_1238` - :ref:`list_software_Coreutils_954` - :ref:`list_software_corner_649` - :ref:`list_software_coverage_844` - :ref:`list_software_cowsay_662` - :ref:`list_software_CP2K_272` - :ref:`list_software_CPB_213` - :ref:`list_software_CPLEX_380` - :ref:`list_software_CppUnit_707` - :ref:`list_software_cram_419` - :ref:`list_software_cramtools_980` - :ref:`list_software_CrayCCE_602` - :ref:`list_software_CrayGNU_633` - :ref:`list_software_CrayIntel_907` - :ref:`list_software_CrayPGI_623` - :ref:`list_software_crb-blast_890` - :ref:`list_software_CRF++_305` - :ref:`list_software_CrossMap_808` - :ref:`list_software_CrossTalkZ_1008` - :ref:`list_software_CRPropa_663` - :ref:`list_software_CryptoMiniSat_1334` - :ref:`list_software_CSBDeep_598` - :ref:`list_software_cscope_637` - :ref:`list_software_csvkit_660` - :ref:`list_software_ctags_530` - :ref:`list_software_ctffind_734` - :ref:`list_software_Cube_383` - :ref:`list_software_CubeGUI_612` - :ref:`list_software_CubeLib_662` - :ref:`list_software_CubeWriter_1020` - :ref:`list_software_CUDA_285` - :ref:`list_software_cuDNN_440` - :ref:`list_software_Cufflinks_933` - :ref:`list_software_CUnit_483` - :ref:`list_software_cURL_342` - :ref:`list_software_custodian_970` - :ref:`list_software_cutadapt_854` - :ref:`list_software_CVS_236` - :ref:`list_software_CVXOPT_484` - :ref:`list_software_CVXPY_410` - :ref:`list_software_cysignals_973` - :ref:`list_software_Cython_629` - :ref:`list_software_cytoolz_788` - :ref:`list_software_cytosim_776` - :ref:`list_software_cyvcf2_589` .. _list_software_C3D_186: *C3D* +++++ Convert3D Medical Image Processing Tool *homepage*: https://sourceforge.net/projects/c3d/ ========= ========== version toolchain ========= ========== ``1.0.0`` ``system`` ========= ========== .. _list_software_cadaver_726: *cadaver* +++++++++ cadaver is a command-line WebDAV client for Unix. *homepage*: http://www.webdav.org/cadaver/ ========== =============== version toolchain ========== =============== ``0.23.3`` ``intel/2017a`` ========== =============== .. _list_software_Caffe_469: *Caffe* +++++++ Caffe is a deep learning framework made with expression, speed, and modularity in mind. It is developed by the Berkeley Vision and Learning Center (BVLC) and community contributors. *homepage*: https://github.com/BVLC/caffe ======= ============================== =============== version versionsuffix toolchain ======= ============================== =============== ``1.0`` ``-CUDA-9.1.85-Python-2.7.14`` ``intel/2017b`` ``1.0`` ``-Python-2.7.13`` ``intel/2017a`` ``1.0`` ``-Python-2.7.14`` ``intel/2017b`` ``rc3`` ``-CUDA-7.5.18-Python-2.7.11`` ``foss/2016a`` ======= ============================== =============== .. _list_software_cairo_526: *cairo* +++++++ Cairo is a 2D graphics library with support for multiple output devices. Currently supported output targets include the X Window System (via both Xlib and XCB), Quartz, Win32, image buffers, PostScript, PDF, and SVG file output. Experimental backends include OpenGL, BeOS, OS/2, and DirectFB *homepage*: https://cairographics.org =========== ================ ================================================================ version versionsuffix toolchain =========== ================ ================================================================ ``1.14.6`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.14.6`` ``-GLib-2.48.0`` ``foss/2016a``, ``intel/2016a`` ``1.14.8`` ``intel/2017a`` ``1.14.10`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017b`` ``1.14.12`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.16.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` =========== ================ ================================================================ .. _list_software_cairomm_744: *cairomm* +++++++++ The Cairomm package provides a C++ interface to Cairo. *homepage*: http://cairographics.org ========== ==================================== version toolchain ========== ==================================== ``1.12.2`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ========== ==================================== .. _list_software_Calendrical_1106: *Calendrical* +++++++++++++ Calendrical module is for calendrical calculations. *homepage*: https://www.funaba.org/code#calendrical ========== ================= =============== version versionsuffix toolchain ========== ================= =============== ``2.0.1`` ``-Python-3.6.3`` ``intel/2017b`` ``2.0.2a`` ``-Python-3.6.4`` ``intel/2018a`` ``2.0.2a`` ``-Python-3.6.6`` ``intel/2018b`` ========== ================= =============== .. _list_software_Cantera_702: *Cantera* +++++++++ Chemical kinetics, thermodynamics, and transport tool suite *homepage*: https://github.com/Cantera/cantera ========= ================== ================================================ version versionsuffix toolchain ========= ================== ================================================ ``2.2.1`` ``-Python-2.7.12`` ``intel/2016b`` ``2.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``2.3.0`` ``-Python-2.7.13`` ``intel/2017a`` ``2.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``2.4.0`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== ================================================ .. _list_software_canu_423: *canu* ++++++ Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing *homepage*: http://canu.readthedocs.io ======= ================ =============================== version versionsuffix toolchain ======= ================ =============================== ``1.4`` ``foss/2016b`` ``1.7`` ``intel/2018a`` ``1.8`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``1.8`` ``-Perl-5.28.0`` ``foss/2018b`` ``1.8`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` ======= ================ =============================== .. _list_software_Canvas_604: *Canvas* ++++++++ Copy number variant (CNV) calling from DNA sequencing data *homepage*: https://github.com/Illumina/canvas =============== ========== version toolchain =============== ========== ``1.39.0.1598`` ``system`` =============== ========== .. _list_software_CAP3_263: *CAP3* ++++++ CAP3 assembly program *homepage*: http://seq.cs.iastate.edu/ ========================= ========== version toolchain ========================= ========== ``20071221-intel-x86`` ``system`` ``20071221-intel-x86_64`` ``system`` ``20071221-opteron`` ``system`` ========================= ========== .. _list_software_CapnProto_918: *CapnProto* +++++++++++ Cap’n Proto is an insanely fast data interchange format and capability-based RPC system. *homepage*: https://capnproto.org ========= ================= version toolchain ========= ================= ``0.6.1`` ``GCCcore/6.4.0`` ``0.7.0`` ``GCCcore/7.3.0`` ========= ================= .. _list_software_Cargo_492: *Cargo* +++++++ The Rust package manager *homepage*: https://crates.io/ ========== ============== version toolchain ========== ============== ``0.13.0`` ``foss/2016b`` ========== ============== .. _list_software_CastXML_636: *CastXML* +++++++++ CastXML is a C-family abstract syntax tree XML output tool. *homepage*: https://github.com/CastXML/CastXML ============ ============== version toolchain ============ ============== ``20160617`` ``foss/2016a`` ``20180806`` ``foss/2018a`` ============ ============== .. _list_software_Catch2_533: *Catch2* ++++++++ A modern, C++-native, header-only, test framework for unit-tests, TDD and BDD - using C++11, C++14, C++17 and later (or C++03 on the Catch1.x branch) *homepage*: https://github.com/catchorg/Catch2 ========== ========== version toolchain ========== ========== ``2.9.1`` ``system`` ``2.11.0`` ``system`` ========== ========== .. _list_software_CatMAP_502: *CatMAP* ++++++++ Catalyst Micro-kinetic Analysis Package for automated creation of micro-kinetic models used in catalyst screening. *homepage*: http://catmap.readthedocs.io/ ============ ================== =============== version versionsuffix toolchain ============ ================== =============== ``20170927`` ``-Python-2.7.14`` ``intel/2017b`` ============ ================== =============== .. _list_software_causalml_850: *causalml* ++++++++++ Causal ML: A Python Package for Uplift Modeling and Causal Inference with ML *homepage*: https://github.com/uber/causalml ================== ================= ============== version versionsuffix toolchain ================== ================= ============== ``0.3.0-20180610`` ``-Python-3.7.2`` ``foss/2019a`` ================== ================= ============== .. _list_software_CaVEMan_603: *CaVEMan* +++++++++ SNV expectation maximisation based mutation calling algorithm aimed at detecting somatic mutations in paired (tumour/normal) cancer samples. Supports both bam and cram format via htslib *homepage*: http://cancerit.github.io/CaVEMan/ ========== ============== version toolchain ========== ============== ``1.13.2`` ``foss/2018a`` ========== ============== .. _list_software_CBLAS_357: *CBLAS* +++++++ C interface to the BLAS *homepage*: http://www.netlib.org/blas/ ============ ============== version toolchain ============ ============== ``20110120`` ``foss/2016b`` ============ ============== .. _list_software_ccache_599: *ccache* ++++++++ Cache for C/C++ compilers *homepage*: http://ccache.samba.org/ ========= ============= ========== version versionsuffix toolchain ========= ============= ========== ``3.2.5`` ``system`` ``3.3.1`` ``system`` ``3.3.3`` ``system`` ``3.3.4`` ``-f90`` ``system`` ========= ============= ========== .. _list_software_CCL_210: *CCL* +++++ Clozure CL (often called CCL for short) is a free Common Lisp implementation with a long history. Some distinguishing features of the implementation include fast compilation speed, native threads, a precise, generational, compacting garbage collector, and a convenient foreign-function interface. *homepage*: https://ccl.clozure.com/ ========== ========== version toolchain ========== ========== ``1.11.5`` ``system`` ========== ========== .. _list_software_cclib_509: *cclib* +++++++ cclib is a Python library that provides parsers for computational chemistry log files. It alsoprovides a platform to implement algorithms in a package-independent manner. *homepage*: http://cclib.github.io/ ======= ================= ============== version versionsuffix toolchain ======= ================= ============== ``1.5`` ``-Python-3.5.2`` ``foss/2016b`` ======= ================= ============== .. _list_software_CD-HIT_409: *CD-HIT* ++++++++ CD-HIT is a very widely used program for clustering and comparing protein or nucleotide sequences. *homepage*: http://weizhong-lab.ucsd.edu/cd-hit/ ========= ============== ================================================ version versionsuffix toolchain ========= ============== ================================================ ``4.6.4`` ``-2015-0603`` ``GNU/4.9.3-2.25`` ``4.6.6`` ``foss/2016b`` ``4.6.8`` ``foss/2018b``, ``intel/2017a``, ``intel/2018a`` ``4.8.1`` ``foss/2018b`` ========= ============== ================================================ .. _list_software_cDNA_Cupcake_1105: *cDNA_Cupcake* ++++++++++++++ cDNA_Cupcake is a miscellaneous collection of Python and R scripts used for analyzing sequencing data. *homepage*: https://github.com/Magdoll/cDNA_Cupcake ======= ================== =============== version versionsuffix toolchain ======= ================== =============== ``5.8`` ``-Python-2.7.14`` ``intel/2018a`` ======= ================== =============== .. _list_software_CDO_214: *CDO* +++++ CDO is a collection of command line Operators to manipulate and analyse Climate and NWP model Data. *homepage*: https://code.zmaw.de/projects/cdo ========= ================================================= version toolchain ========= ================================================= ``1.7.2`` ``intel/2016b`` ``1.8.1`` ``intel/2017a`` ``1.9.1`` ``intel/2017b`` ``1.9.2`` ``intel/2017b`` ``1.9.5`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``1.9.8`` ``intel/2019b`` ========= ================================================= .. _list_software_cdsapi_628: *cdsapi* ++++++++ Climate Data Store API *homepage*: https://pypi.org/project/cdsapi ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``0.1.4`` ``foss/2019a`` ``0.1.4`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== .. _list_software_CellMix_686: *CellMix* +++++++++ A Comprehensive Toolbox for Gene Expression Deconvolution *homepage*: http://web.cbio.uct.ac.za/~renaud/CRAN/web/CellMix ========= ============= ============== version versionsuffix toolchain ========= ============= ============== ``1.6.2`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== .. _list_software_CellRanger_991: *CellRanger* ++++++++++++ Cell Ranger is a set of analysis pipelines that process Chromium single-cell RNA-seq output to align reads, generate gene-cell matrices and perform clustering and gene expression analysis. *homepage*: https://support.10xgenomics.com/single-cell-gene-expression/software/pipelines/latest/what-is-cell-ranger ========= ========== version toolchain ========= ========== ``3.0.0`` ``system`` ``3.0.2`` ``system`` ``3.1.0`` ``system`` ========= ========== .. _list_software_Centrifuge_1036: *Centrifuge* ++++++++++++ Classifier for metagenomic sequences *homepage*: https://ccb.jhu.edu/software/centrifuge/ ============== ============== version toolchain ============== ============== ``1.0.3`` ``foss/2018b`` ``1.0.4-beta`` ``foss/2018b`` ============== ============== .. _list_software_CESM-deps_769: *CESM-deps* +++++++++++ CESM is a fully-coupled, community, global climate model that provides state-of-the-art computer simulations of the Earth's past, present, and future climate states. *homepage*: http://www.cesm.ucar.edu/models/cesm2/ ======= ================================================ version toolchain ======= ================================================ ``2`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` ======= ================================================ .. _list_software_CFITSIO_529: *CFITSIO* +++++++++ CFITSIO is a library of C and Fortran subroutines for reading and writing data files in FITS (Flexible Image Transport System) data format. *homepage*: https://heasarc.gsfc.nasa.gov/fitsio/ ======== ===================================================== version toolchain ======== ===================================================== ``3.38`` ``foss/2016a``, ``intel/2016a`` ``3.41`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``intel/2016b`` ``3.42`` ``GCCcore/6.4.0``, ``intel/2017b`` ``3.45`` ``GCCcore/7.3.0``, ``intel/2018b`` ``3.47`` ``GCCcore/8.2.0`` ======== ===================================================== .. _list_software_cftime_632: *cftime* ++++++++ Time-handling functionality from netcdf4-python *homepage*: https://github.com/Unidata/cftime =========== ================== =============================== version versionsuffix toolchain =========== ================== =============================== ``1.0.0`` ``-Python-3.6.4`` ``intel/2018a`` ``1.0.0b1`` ``-Python-3.6.2`` ``foss/2017b`` ``1.0.1`` ``-Python-2.7.15`` ``intel/2018b`` ``1.0.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` =========== ================== =============================== .. _list_software_CGAL_279: *CGAL* ++++++ The goal of the CGAL Open Source Project is to provide easy access to efficient and reliable geometric algorithms in the form of a C++ library. *homepage*: http://www.cgal.org/ ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``4.8`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``4.8.1`` ``foss/2016b``, ``intel/2016b`` ``4.8.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``4.9`` ``-Python-2.7.12`` ``intel/2016b`` ``4.9`` ``-Python-2.7.13`` ``intel/2017a`` ``4.11`` ``-Python-2.7.13`` ``intel/2017a`` ``4.11`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``4.11`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``4.11.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``4.11.1`` ``-Python-2.7.15`` ``foss/2018b`` ``4.11.1`` ``-Python-3.6.4`` ``foss/2018a`` ``4.11.1`` ``-Python-3.6.6`` ``foss/2018b`` ``4.14`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``4.14.1`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================== =============================== .. _list_software_cget_419: *cget* ++++++ Cmake package retrieval. This can be used to download and install cmake packages *homepage*: https://cget.readthedocs.io/en/latest/index.html ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``0.1.6`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================= ============== .. _list_software_CGNS_299: *CGNS* ++++++ The CGNS system is designed to facilitate the exchange of data between sites and applications, and to help stabilize the archiving of aerodynamic data. *homepage*: https://cgns.github.io/ ========= ============== version toolchain ========= ============== ``3.3.1`` ``foss/2016b`` ========= ============== .. _list_software_CharLS_541: *CharLS* ++++++++ CharLS is a C++ implementation of the JPEG-LS standard for lossless and near-lossless image compression and decompression. JPEG-LS is a low-complexity image compression standard that matches JPEG 2000 compression ratios. *homepage*: https://github.com/team-charls/charls ========= ==================================== version toolchain ========= ==================================== ``2.0.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ========= ==================================== .. _list_software_charmm_632: *charmm* ++++++++ CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. charmm provides all the functionality of CHARMM except its performance enhancements. *homepage*: http://www.charmm.org ======== =============================== version toolchain ======== =============================== ``43b2`` ``foss/2017b``, ``intel/2017b`` ======== =============================== .. _list_software_CHARMM_440: *CHARMM* ++++++++ CHARMM (Chemistry at HARvard Macromolecular Mechanics) is a versatile and widely used molecular simulation program with broad application to many-particle systems. *homepage*: http://www.charmm.org ======== =============================== version toolchain ======== =============================== ``37b2`` ``foss/2016a``, ``intel/2016a`` ======== =============================== .. _list_software_CHASE_356: *CHASE* +++++++ Case-control HAplotype Sharing analyses. Haplotype sharing analyses for genome-wide association studies. *homepage*: http://people.duke.edu/~asallen/Software.html ============ ========== version toolchain ============ ========== ``20130626`` ``system`` ============ ========== .. _list_software_CheckM_555: *CheckM* ++++++++ CheckM provides a set of tools for assessing the quality of genomes recovered from isolates, single cells, or metagenomes. *homepage*: https://github.com/Ecogenomics/CheckM ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``1.0.13`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.0.13`` ``-Python-2.7.15`` ``foss/2018b`` ``1.0.13`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.0.18`` ``-Python-2.7.15`` ``foss/2019a`` ========== ================== =============================== .. _list_software_Cheetah_690: *Cheetah* +++++++++ Cheetah is an open source template engine and code generation tool. *homepage*: http://cheetahtemplate.org ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``2.4.4`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============== .. _list_software_CheMPS2_562: *CheMPS2* +++++++++ CheMPS2 is a scientific library which contains a spin-adapted implementation of the density matrix renormalization group (DMRG) for ab initio quantum chemistry. *homepage*: https://github.com/SebWouters/CheMPS2 =========== ================================================================ version toolchain =========== ================================================================ ``1.6`` ``intel/2016a`` ``1.7.1`` ``intel/2016a`` ``1.7.2`` ``intel/2016a`` ``1.7-rc2`` ``intel/2016a`` ``1.8`` ``intel/2016b`` ``1.8.8`` ``intel/2018b`` ``1.8.9`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` =========== ================================================================ .. _list_software_Chimera_697: *Chimera* +++++++++ UCSF Chimera is a highly extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. *homepage*: https://www.cgl.ucsf.edu/chimera/ ======== ================= ========== version versionsuffix toolchain ======== ================= ========== ``1.10`` ``-linux_x86_64`` ``system`` ======== ================= ========== .. _list_software_ChimPipe_783: *ChimPipe* ++++++++++ ChimPipe is a computational method for the detection of novel transcription-induced chimeric transcripts and fusion genes from Illumina Paired-End RNA-seq data. It combines junction spanning and paired-end read information to accurately detect chimeric splice junctions at base-pair resolution. *homepage*: https://chimpipe.readthedocs.org/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``0.9.5`` ``foss/2018b`` ``0.9.5`` ``-Python-2.7.12`` ``foss/2016b`` ========= ================== ============== .. _list_software_Chromaprint_1159: *Chromaprint* +++++++++++++ Chromaprint is the core component of the AcoustID project. It's a client-side library that implements a custom algorithm for extracting fingerprints from any audio source. *homepage*: https://acoustid.org/chromaprint ========= ================= version toolchain ========= ================= ``1.4.3`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_CIRCexplorer_1170: *CIRCexplorer* ++++++++++++++ CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. *homepage*: http://circexplorer2.readthedocs.io/ ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``1.1.10`` ``-Python-2.7.14`` ``intel/2017b`` ========== ================== =============== .. _list_software_CIRCexplorer2_1220: *CIRCexplorer2* +++++++++++++++ CIRCexplorer2 is a comprehensive and integrative circular RNA analysis toolset. *homepage*: http://circexplorer2.readthedocs.io/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``2.3.2`` ``-Python-2.7.14`` ``intel/2017b`` ``2.3.3`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============== .. _list_software_Circos_611: *Circos* ++++++++ Circos is a software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions. *homepage*: http://www.circos.ca/ ========== ================ ================= version versionsuffix toolchain ========== ================ ================= ``0.69-5`` ``-Perl-5.24.0`` ``foss/2016b`` ``0.69-6`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` ``0.69-6`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` ========== ================ ================= .. _list_software_CIRI_295: *CIRI* ++++++ CircRNA Identifier. A de novo circular RNA identification tool *homepage*: https://sourceforge.net/projects/ciri/ ========= ================ =============== version versionsuffix toolchain ========= ================ =============== ``2.0.6`` ``-Perl-5.26.0`` ``intel/2017b`` ========= ================ =============== .. _list_software_cisTEM_549: *cisTEM* ++++++++ cisTEM is user-friendly software to process cryo-EM images of macromolecular complexes and obtain high-resolution 3D reconstructions from them. *homepage*: https://cistem.org/ ============== ============== version toolchain ============== ============== ``1.0.0-beta`` ``foss/2018a`` ============== ============== .. _list_software_CITE-seq-Count_1233: *CITE-seq-Count* ++++++++++++++++ A python package that allows to count antibody TAGS from a CITE-seq and/or cell hashing experiment. *homepage*: https://github.com/Hoohm/CITE-seq-Count ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== .. _list_software_Clang_485: *Clang* +++++++ C, C++, Objective-C compiler, based on LLVM. Does not include C++ standard library -- use libstdc++ from GCC. *homepage*: https://clang.llvm.org/ ========= ================== ====================================== version versionsuffix toolchain ========= ================== ====================================== ``3.3`` ``GCC/4.8.1`` ``3.4`` ``GCC/4.8.2`` ``3.4.1`` ``GCC/4.8.2`` ``3.4.2`` ``GCC/4.8.2`` ``3.6.0`` ``GCC/4.9.2`` ``3.6.1`` ``GCC/4.9.2`` ``3.7.0`` ``GNU/4.9.3-2.25`` ``3.7.1`` ``GCC/4.9.3-2.25``, ``foss/2016a`` ``3.8.0`` ``GCC/4.9.3-2.25`` ``3.8.1`` ``GCC/5.4.0-2.26``, ``foss/2016b`` ``5.0.0`` ``GCC/6.4.0-2.28`` ``5.0.1`` ``GCC/6.4.0-2.28`` ``6.0.1`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30`` ``7.0.0`` ``GCC/6.4.0-2.28`` ``7.0.1`` ``GCC/7.3.0-2.30`` ``8.0.0`` ``GCCcore/8.2.0`` ``8.0.0`` ``-CUDA-10.1.105`` ``GCCcore/8.2.0`` ``9.0.1`` ``GCCcore/8.3.0`` ``9.0.1`` ``-CUDA-10.1.243`` ``GCC/8.3.0`` ========= ================== ====================================== .. _list_software_Clang-Python-bindings_2063: *Clang-Python-bindings* +++++++++++++++++++++++ Python bindings for libclang *homepage*: https://clang.llvm.org ========= ================== ================= version versionsuffix toolchain ========= ================== ================= ``8.0.0`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ========= ================== ================= .. _list_software_CLAPACK_495: *CLAPACK* +++++++++ C version of LAPACK *homepage*: http://www.netlib.org/clapack ========= =========================================================================== version toolchain ========= =========================================================================== ``3.2.1`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a`` ========= =========================================================================== .. _list_software_CLHEP_364: *CLHEP* +++++++ The CLHEP project is intended to be a set of HEP-specific foundation and utility classes such as random generators, physics vectors, geometry and linear algebra. CLHEP is structured in a set of packages independent of any external package. *homepage*: http://proj-clhep.web.cern.ch/proj-clhep/ =========== ================================================================ version toolchain =========== ================================================================ ``2.1.1.0`` ``intel/2016a`` ``2.1.3.1`` ``intel/2016a`` ``2.2.0.8`` ``intel/2016a`` ``2.3.1.1`` ``intel/2016a`` ``2.3.4.3`` ``foss/2017b``, ``intel/2017b`` ``2.4.0.0`` ``intel/2017b`` ``2.4.1.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018b`` =========== ================================================================ .. _list_software_CLISP_379: *CLISP* +++++++ Common Lisp is a high-level, general-purpose, object-oriented, dynamic, functional programming language. *homepage*: http://www.clisp.org/ ======== ================= version toolchain ======== ================= ``2.49`` ``GCCcore/6.4.0`` ======== ================= .. _list_software_ClonalFrameML_1245: *ClonalFrameML* +++++++++++++++ Efficient Inference of Recombination in Whole Bacterial Genomes *homepage*: https://github.com/xavierdidelot/ClonalFrameML ======== ============== version toolchain ======== ============== ``1.11`` ``foss/2016b`` ======== ============== .. _list_software_CLooG_436: *CLooG* +++++++ CLooG is a free software and library to generate code for scanning Z-polyhedra. That is, it finds a code (e.g. in C, FORTRAN...) that reaches each integral point of one or more parameterized polyhedra. CLooG has been originally written to solve the code generation problem for optimizing compilers based on the polytope model. Nevertheless it is used now in various area e.g. to build control automata for high-level synthesis or to find the best polynomial approximation of a function. CLooG may help in any situation where scanning polyhedra matters. While the user has full control on generated code quality, CLooG is designed to avoid control overhead and to produce a very effective code. *homepage*: http://www.bastoul.net/cloog/index.php ========== ============= version toolchain ========== ============= ``0.18.1`` ``GCC/4.8.2`` ========== ============= .. _list_software_Clustal-Omega_1262: *Clustal-Omega* +++++++++++++++ Clustal Omega is a multiple sequence alignment program for proteins. It produces biologically meaningful multiple sequence alignments of divergent sequences. Evolutionary relationships can be seen via viewing Cladograms or Phylograms *homepage*: http://www.clustal.org/omega/ ========= ================================================ version toolchain ========= ================================================ ``1.2.0`` ``foss/2016b`` ``1.2.4`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` ========= ================================================ .. _list_software_ClustalW2_865: *ClustalW2* +++++++++++ ClustalW2 is a general purpose multiple sequence alignment program for DNA or proteins. *homepage*: http://www.ebi.ac.uk/Tools/msa/clustalw2/ ======= ========================================================================================================== version toolchain ======= ========================================================================================================== ``2.1`` ``foss/2016b``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017b``, ``intel/2018b`` ======= ========================================================================================================== .. _list_software_Cluster-Buster_1412: *Cluster-Buster* ++++++++++++++++ Cluster-Buster: Finding dense clusters of motifs in DNA sequences *homepage*: https://github.com/weng-lab/cluster-buster/ ============ =============== version toolchain ============ =============== ``20160106`` ``intel/2016a`` ============ =============== .. _list_software_ClusterShell_1242: *ClusterShell* ++++++++++++++ ClusterShell is an event-driven open source Python library, designed to run local or distant commands in parallel on server farms or on large Linux clusters. *homepage*: http://cea-hpc.github.io/clustershell/ ========= ========== version toolchain ========= ========== ``1.7.3`` ``system`` ========= ========== .. _list_software_CMake_449: *CMake* +++++++ CMake, the cross-platform, open-source build system. CMake is a family of tools designed to build, test and package software. *homepage*: https://www.cmake.org ========== ================================================================================================================================================= version toolchain ========== ================================================================================================================================================= ``2.8.11`` ``GCC/4.8.1`` ``2.8.12`` ``GCC/4.8.1``, ``GCC/4.8.2`` ``3.0.0`` ``GCC/4.8.3`` ``3.1.0`` ``GCC/4.9.2`` ``3.1.3`` ``GCC/4.9.2``, ``system`` ``3.2.1`` ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` ``3.3.1`` ``system`` ``3.3.2`` ``GNU/4.9.3-2.25``, ``gimkl/2.11.5`` ``3.4.1`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``foss/2016a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``3.4.3`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a`` ``3.5.1`` ``intel/2016a`` ``3.5.2`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``system`` ``3.6.1`` ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``foss/2016b``, ``intel/2016b``, ``system`` ``3.6.2`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` ``3.7.1`` ``GCCcore/5.4.0``, ``GCCcore/6.2.0``, ``foss/2016b``, ``intel/2016b`` ``3.7.2`` ``GCCcore/6.3.0``, ``foss/2016b``, ``intel/2016b`` ``3.8.0`` ``GCCcore/6.3.0`` ``3.8.1`` ``GCCcore/6.3.0`` ``3.8.2`` ``GCCcore/6.3.0`` ``3.9.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``system`` ``3.9.4`` ``GCCcore/6.4.0`` ``3.9.5`` ``GCCcore/6.4.0`` ``3.9.6`` ``system`` ``3.10.0`` ``GCCcore/6.4.0`` ``3.10.1`` ``GCCcore/6.4.0`` ``3.10.2`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` ``3.10.3`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0`` ``3.11.1`` ``GCCcore/6.4.0`` ``3.11.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``3.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``system`` ``3.13.3`` ``GCCcore/8.2.0`` ``3.15.3`` ``GCCcore/8.3.0`` ========== ================================================================================================================================================= .. _list_software_CNT-ILP_503: *CNT-ILP* +++++++++ Integer Linear Program for the Copy-Number Tree Problem *homepage*: https://compbio.cs.brown.edu/projects/cnt-ilp/ ============ ==================== version toolchain ============ ==================== ``20171031`` ``GCC/8.2.0-2.31.1`` ============ ==================== .. _list_software_CNVkit_559: *CNVkit* ++++++++ A command-line toolkit and Python library for detecting copy number variants and alterations genome-wide from high-throughput sequencing. *homepage*: http://github.com/etal/cnvkit ========= ========================= =============== version versionsuffix toolchain ========= ========================= =============== ``0.9.2`` ``-Python-2.7.14`` ``intel/2017b`` ``0.9.6`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a`` ========= ========================= =============== .. _list_software_CNVnator_779: *CNVnator* ++++++++++ a tool for CNV discovery and genotyping from depth-of-coverage by mapped reads *homepage*: https://github.com/abyzovlab/CNVnator ========= ============== version toolchain ========= ============== ``0.3.3`` ``foss/2016b`` ========= ============== .. _list_software_CODEX2_421: *CODEX2* ++++++++ Full-spectrum copy number variation detection by high-throughput DNA sequencing *homepage*: https://github.com/yuchaojiang/CODEX2 ============ ============= =============== version versionsuffix toolchain ============ ============= =============== ``20180227`` ``-R-3.4.3`` ``intel/2017b`` ============ ============= =============== .. _list_software_Commet_613: *Commet* ++++++++ COMMET ("COmpare Multiple METagenomes") provides a global similarity overview between all datasets of a large metagenomic project. *homepage*: https://colibread.inria.fr/software/commet/ ============ ================== ============== version versionsuffix toolchain ============ ================== ============== ``20150415`` ``-Python-2.7.11`` ``foss/2016a`` ============ ================== ============== .. _list_software_Con3F_409: *Con3F* +++++++ Con3F is a Python package to read, manipulate and convert force field files *homepage*: https://github.ugent.be/CMM/con3f ================ ================= =============== version versionsuffix toolchain ================ ================= =============== ``1.0-20190329`` ``-Python-3.7.2`` ``intel/2019a`` ================ ================= =============== .. _list_software_CONCOCT_521: *CONCOCT* +++++++++ Clustering cONtigs with COverage and ComposiTion (CONCOCT) is a program for unsupervised binning of metagenomic contigs by using nucleotide composition, coverage data in multiple samples and linkage data from paired end reads. *homepage*: https://concoct.readthedocs.io ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.0.0`` ``-Python-2.7.14`` ``foss/2017b`` ``1.0.0`` ``-Python-2.7.15`` ``foss/2018b`` ``1.0.0`` ``-Python-3.6.3`` ``foss/2017b`` ``1.1.0`` ``-Python-2.7.15`` ``foss/2019a`` ========= ================== ============== .. _list_software_configparser_1283: *configparser* ++++++++++++++ configparser is a Python library that brings the updated configparser from Python 3.5 to Python 2.6-3.5 *homepage*: http://docs.python.org/3/library/configparser.html ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``3.5.0`` ``-Python-2.7.11`` ``foss/2016a`` ``3.5.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``3.5.0`` ``-Python-3.5.2`` ``intel/2016b`` ``3.5.0`` ``-Python-3.6.3`` ``intel/2017b`` ========= ================== =============================== .. _list_software_configurable-http-proxy_2381: *configurable-http-proxy* +++++++++++++++++++++++++ HTTP proxy for node.js including a REST API for updating the routing table. Developed as a part of the Jupyter Hub multi-user server. *homepage*: https://github.com/jupyterhub/configurable-http-proxy ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``1.3.0`` ``-nodejs-4.4.7`` ``foss/2016a`` ``3.1.1`` ``-nodejs-8.9.4`` ``foss/2017a`` ========= ================= ============== .. _list_software_ConnectomeWorkbench_1966: *ConnectomeWorkbench* +++++++++++++++++++++ Connectome Workbench is an open source, freely available visualization and discovery tool used to map neuroimaging data, especially data generated by the Human Connectome Project. *homepage*: https://www.humanconnectome.org/software/connectome-workbench ========= ================================================== version toolchain ========= ================================================== ``1.2.2`` ``system`` ``1.3.2`` ``GCCcore/8.2.0``, ``foss/2017b``, ``intel/2017b`` ========= ================================================== .. _list_software_Control-FREEC_1139: *Control-FREEC* +++++++++++++++ Copy number and genotype annotation from whole genome and whole exome sequencing data. *homepage*: https://github.com/BoevaLab/FREEC ======== ==================== version toolchain ======== ==================== ``11.5`` ``GCC/8.2.0-2.31.1`` ======== ==================== .. _list_software_CoordgenLibs_1211: *CoordgenLibs* ++++++++++++++ Schrodinger-developed 2D Coordinate Generation *homepage*: https://github.com/schrodinger/coordgenlibs ========= ================================ version toolchain ========= ================================ ``1.3.2`` ``gompi/2019a``, ``iimpi/2019a`` ========= ================================ .. _list_software_Coot_405: *Coot* ++++++ Coot is for macromolecular model building, model completion and validation, particularly suitable for protein modelling using X-ray data. *homepage*: http://www2.mrc-lmb.cam.ac.uk/Personal/pemsley/coot ========= =========================================== ========== version versionsuffix toolchain ========= =========================================== ========== ``0.8.1`` ``-binary-Linux-x86_64-rhel-6-python-gtk2`` ``system`` ========= =========================================== ========== .. _list_software_core-counter_1238: *core-counter* ++++++++++++++ Tool to check available cores and OMP threads *homepage*: https://github.com/gjbex/core-counter ========= ========== version toolchain ========= ========== ``1.1.1`` ``system`` ========= ========== .. _list_software_Coreutils_954: *Coreutils* +++++++++++ The GNU Core Utilities are the basic file, shell and text manipulation utilities of the GNU operating system. These are the core utilities which are expected to exist on every operating system. *homepage*: http://www.gnu.org/software/coreutils/ ======== ================= version toolchain ======== ================= ``8.23`` ``GCC/4.9.2`` ``8.27`` ``GCCcore/5.4.0`` ``8.29`` ``GCCcore/6.4.0`` ======== ================= .. _list_software_corner_649: *corner* ++++++++ Make some beautiful corner plots. *homepage*: https://corner.readthedocs.io/en/latest/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.0.1`` ``-Python-2.7.15`` ``foss/2019a`` ``2.0.1`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================== ============== .. _list_software_coverage_844: *coverage* ++++++++++ Coverage.py is a tool for measuring code coverage of Python programs. It monitors your program, noting which parts of the code have been executed, then analyzes the source to identify code that could have been executed but was not. *homepage*: https://coverage.readthedocs.io ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``4.5.1`` ``-Python-2.7.14`` ``intel/2017b`` ========= ================== =============== .. _list_software_cowsay_662: *cowsay* ++++++++ Configurable talking characters in ASCII art *homepage*: https://github.com/tnalpgge/rank-amateur-cowsay ======== ========== version toolchain ======== ========== ``3.04`` ``system`` ======== ========== .. _list_software_CP2K_272: *CP2K* ++++++ CP2K is a freely available (GPL) program, written in Fortran 95, to perform atomistic and molecular simulations of solid state, liquid, molecular and biological systems. It provides a general framework for different methods such as e.g. density functional theory (DFT) using a mixed Gaussian and plane waves approach (GPW), and classical pair and many-body potentials. *homepage*: http://www.cp2k.org/ ======= ============= ================================================================== version versionsuffix toolchain ======= ============= ================================================================== ``3.0`` ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` ``3.0`` ``-psmp`` ``intel/2016b`` ``4.1`` ``intel/2016b`` ``4.1`` ``-psmp`` ``foss/2016b`` ``5.1`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``6.1`` ``foss/2019a``, ``intel/2018a`` ======= ============= ================================================================== .. _list_software_CPB_213: *CPB* +++++ CPB is a novel two-step Pearson correlation based biclustering approach to mine genes that are co-regulated with a given reference gene in order to discover genes that function in a common biological process. In the first step, the algorithm identifies subsets of genes with high correlation, reducing false negatives with a nonparametric filtering scheme. In the second step, biclusters from multiple datasets are used to extract and rank gene correlation information. *homepage*: http://tda.gatech.edu/software/cpb/index.html ============= ================== ============== version versionsuffix toolchain ============= ================== ============== ``11-4-2011`` ``-Python-2.7.13`` ``foss/2017a`` ============= ================== ============== .. _list_software_CPLEX_380: *CPLEX* +++++++ IBM ILOG CPLEX Optimizer's mathematical programming technology enables analytical decision support for improving efficiency, reducing costs, and increasing profitability. *homepage*: https://www.ibm.com/analytics/cplex-optimizer ======== ================= version toolchain ======== ================= ``12.9`` ``GCCcore/8.2.0`` ======== ================= .. _list_software_CppUnit_707: *CppUnit* +++++++++ CppUnit is the C++ port of the famous JUnit framework for unit testing. *homepage*: http://sourceforge.net/projects/cppunit/ ========== ==================================================== version toolchain ========== ==================================================== ``1.12.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a`` ========== ==================================================== .. _list_software_cram_419: *cram* ++++++ Cram is a functional testing framework for command line applications. *homepage*: https://bitheap.org/cram ======= ================= version toolchain ======= ================= ``0.7`` ``GCCcore/8.2.0`` ======= ================= .. _list_software_cramtools_980: *cramtools* +++++++++++ CRAMTools is a set of Java tools and APIs for efficient compression of sequence read data. Although this is intended as a stable version the code is released as early access. Parts of the CRAMTools are experimental and may not be supported in the future. *homepage*: https://github.com/enasequence/cramtools/ ======= ================== ========== version versionsuffix toolchain ======= ================== ========== ``2.0`` ``-Java-1.7.0_80`` ``system`` ``3.0`` ``-Java-1.7.0_80`` ``system`` ======= ================== ========== .. _list_software_CrayCCE_602: *CrayCCE* +++++++++ Toolchain using Cray compiler wrapper, using PrgEnv-cray (PE release: June 2019). *homepage*: https://pubs.cray.com/discover ========= ========== version toolchain ========= ========== ``19.06`` ``system`` ========= ========== .. _list_software_CrayGNU_633: *CrayGNU* +++++++++ Toolchain using Cray compiler wrapper, using PrgEnv-gnu module (PE release: June 2019). *homepage*: https://pubs.cray.com/discover ========= ========== version toolchain ========= ========== ``19.06`` ``system`` ========= ========== .. _list_software_CrayIntel_907: *CrayIntel* +++++++++++ Toolchain using Cray compiler wrapper, using PrgEnv-intel (PE release: June 2019). *homepage*: https://pubs.cray.com/discover ========= ========== version toolchain ========= ========== ``19.06`` ``system`` ========= ========== .. _list_software_CrayPGI_623: *CrayPGI* +++++++++ Toolchain using Cray compiler wrapper, PrgEnv-pgi compiler (PE release: June 2019). *homepage*: https://pubs.cray.com/discover ========= ========== version toolchain ========= ========== ``19.06`` ``system`` ========= ========== .. _list_software_crb-blast_890: *crb-blast* +++++++++++ Conditional Reciprocal Best BLAST - high confidence ortholog assignment. CRB-BLAST is a novel method for finding orthologs between one set of sequences and another. This is particularly useful in genome and transcriptome annotation. *homepage*: https://github.com/cboursnell/crb-blast ========= =============== version toolchain ========= =============== ``0.6.9`` ``intel/2017a`` ========= =============== .. _list_software_CRF++_305: *CRF++* +++++++ CRF++ is a simple, customizable, and open source implementation of Conditional Random Fields (CRFs) for segmenting/labeling sequential data. CRF++ is designed for generic purpose and will be applied to a variety of NLP tasks, such as Named Entity Recognition, Information Extraction and Text Chunking. *homepage*: https://taku910.github.io/crfpp/ ======== ========================================================= version toolchain ======== ========================================================= ``0.58`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ======== ========================================================= .. _list_software_CrossMap_808: *CrossMap* ++++++++++ CrossMap is a program for genome coordinates conversion between different assemblies (such as hg18 (NCBI36) <=> hg19 (GRCh37)). It supports commonly used file formats including BAM, CRAM, SAM, Wiggle, BigWig, BED, GFF, GTF and VCF. *homepage*: http://crossmap.sourceforge.net ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``0.3.9`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================= ============== .. _list_software_CrossTalkZ_1008: *CrossTalkZ* ++++++++++++ CrossTalkZ is a statistical method and software to assess the significance of crosstalk enrichment between pairs of gene or protein groups in large biological networks. *homepage*: http://sonnhammer.sbc.su.se/download/software/CrossTalkZ/ ======= ============== version toolchain ======= ============== ``1.4`` ``foss/2016a`` ======= ============== .. _list_software_CRPropa_663: *CRPropa* +++++++++ CRPropa is a publicly available code to study the propagation of ultra high energy nuclei up to iron on their voyage through an extra galactic environment. *homepage*: https://crpropa.desy.de ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``3.1.5`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================= ============== .. _list_software_CryptoMiniSat_1334: *CryptoMiniSat* +++++++++++++++ CryptoMiniSat is an advanced SAT solver *homepage*: https://github.com/msoos/cryptominisat ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``5.0.1`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== .. _list_software_CSBDeep_598: *CSBDeep* +++++++++ CSBDeep is a toolbox for Content-aware Image Restoration (CARE). *homepage*: https://csbdeep.bioimagecomputing.com/ ========= ================= ================================== version versionsuffix toolchain ========= ================= ================================== ``0.4.1`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ========= ================= ================================== .. _list_software_cscope_637: *cscope* ++++++++ Cscope is a developer's tool for browsing source code. *homepage*: http://cscope.sourceforge.net/ ======== ========== version toolchain ======== ========== ``15.9`` ``system`` ======== ========== .. _list_software_csvkit_660: *csvkit* ++++++++ csvkit is a suite of command-line tools for converting to and working with CSV, the king of tabular file formats. *homepage*: https://github.com/wireservice/csvkit ========= ================= version toolchain ========= ================= ``1.0.4`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_ctags_530: *ctags* +++++++ Ctags generates an index (or tag) file of language objects found in source files that allows these items to be quickly and easily located by a text editor or other utility. *homepage*: http://ctags.sourceforge.net/ ======= ========== version toolchain ======= ========== ``5.8`` ``system`` ======= ========== .. _list_software_ctffind_734: *ctffind* +++++++++ Program for finding CTFs of electron micrographs. *homepage*: https://grigoriefflab.umassmed.edu/ctffind4 ========== ================================== version toolchain ========== ================================== ``4.1.13`` ``foss/2019a``, ``fosscuda/2019a`` ========== ================================== .. _list_software_Cube_383: *Cube* ++++++ Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. *homepage*: http://www.scalasca.org/software/cube-4.x/download.html ========= ============== version toolchain ========= ============== ``4.3.4`` ``foss/2016a`` ========= ============== .. _list_software_CubeGUI_612: *CubeGUI* +++++++++ Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube graphical report explorer. *homepage*: https://www.scalasca.org/software/cube-4.x/download.html ========= ================= version toolchain ========= ================= ``4.4.4`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_CubeLib_662: *CubeLib* +++++++++ Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube general purpose C++ library component and command-line tools. *homepage*: https://www.scalasca.org/software/cube-4.x/download.html ========= ================= version toolchain ========= ================= ``4.4.4`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_CubeWriter_1020: *CubeWriter* ++++++++++++ Cube, which is used as performance report explorer for Scalasca and Score-P, is a generic tool for displaying a multi-dimensional performance space consisting of the dimensions (i) performance metric, (ii) call path, and (iii) system resource. Each dimension can be represented as a tree, where non-leaf nodes of the tree can be collapsed or expanded to achieve the desired level of granularity. This module provides the Cube high-performance C writer library component. *homepage*: https://www.scalasca.org/software/cube-4.x/download.html ========= ================= version toolchain ========= ================= ``4.4.3`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_CUDA_285: *CUDA* ++++++ CUDA (formerly Compute Unified Device Architecture) is a parallel computing platform and programming model created by NVIDIA and implemented by the graphics processing units (GPUs) that they produce. CUDA gives developers access to the virtual instruction set and memory of the parallel computational elements in CUDA GPUs. *homepage*: https://developer.nvidia.com/cuda-toolkit ================= ========================================================================== version toolchain ================= ========================================================================== ``5.5.22`` ``GCC/4.8.2``, ``system`` ``6.0.37`` ``system`` ``6.5.14`` ``system`` ``7.0.28`` ``system`` ``7.5.18`` ``GCC/4.9.4-2.25``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``system`` ``8.0.44`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``system`` ``8.0.61`` ``system`` ``8.0.61_375.26`` ``GCC/5.4.0-2.26`` ``9.0.176`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``system`` ``9.1.85`` ``GCC/6.4.0-2.28``, ``system`` ``9.2.88`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30``, ``system`` ``9.2.148.1`` ``system`` ``10.0.130`` ``system`` ``10.1.105`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``system`` ``10.1.168`` ``system`` ``10.1.243`` ``GCC/8.3.0``, ``iccifort/2019.5.281``, ``system`` ``10.2.89`` ``GCC/8.3.0`` ================= ========================================================================== .. _list_software_cuDNN_440: *cuDNN* +++++++ The NVIDIA CUDA Deep Neural Network library (cuDNN) is a GPU-accelerated library of primitives for deep neural networks. *homepage*: https://developer.nvidia.com/cudnn ============ ================== =========================================================== version versionsuffix toolchain ============ ================== =========================================================== ``4.0`` ``system`` ``5.0`` ``-CUDA-7.5.18`` ``system`` ``5.0-rc`` ``system`` ``5.1`` ``-CUDA-8.0.44`` ``system`` ``6.0`` ``-CUDA-8.0.61`` ``system`` ``7.0.2`` ``-CUDA-9.0.176`` ``system`` ``7.0.5`` ``-CUDA-9.1.85`` ``system`` ``7.0.5.15`` ``fosscuda/2017b``, ``fosscuda/2018a``, ``intelcuda/2017b`` ``7.1.4.18`` ``fosscuda/2018b`` ``7.4.2.24`` ``gcccuda/2019a`` ``7.4.2.24`` ``-CUDA-10.0.130`` ``system`` ``7.6.2.24`` ``-CUDA-10.1.243`` ``system`` ``7.6.4.38`` ``gcccuda/2019a``, ``gcccuda/2019b`` ``7.6.4.38`` ``-CUDA-10.0.130`` ``system`` ============ ================== =========================================================== .. _list_software_Cufflinks_933: *Cufflinks* +++++++++++ Transcript assembly, differential expression, and differential regulation for RNA-Seq *homepage*: http://cole-trapnell-lab.github.io/cufflinks/ ============ ================================================================================ version toolchain ============ ================================================================================ ``2.2.1`` ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ``20190706`` ``gompi/2019a`` ============ ================================================================================ .. _list_software_CUnit_483: *CUnit* +++++++ Automated testing framework for C. *homepage*: https://sourceforge.net/projects/cunit/ ========= ================= version toolchain ========= ================= ``2.1-3`` ``GCCcore/6.4.0`` ========= ================= .. _list_software_cURL_342: *cURL* ++++++ libcurl is a free and easy-to-use client-side URL transfer library, supporting DICT, FILE, FTP, FTPS, Gopher, HTTP, HTTPS, IMAP, IMAPS, LDAP, LDAPS, POP3, POP3S, RTMP, RTSP, SCP, SFTP, SMTP, SMTPS, Telnet and TFTP. libcurl supports SSL certificates, HTTP POST, HTTP PUT, FTP uploading, HTTP form based upload, proxies, cookies, user+password authentication (Basic, Digest, NTLM, Negotiate, Kerberos), file transfer resume, http proxy tunneling and more. *homepage*: https://curl.haxx.se ========== =================================================================================== version toolchain ========== =================================================================================== ``7.33.0`` ``GCC/4.8.2`` ``7.34.0`` ``GCC/4.8.2`` ``7.40.0`` ``GCC/4.9.2`` ``7.46.0`` ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``7.47.0`` ``foss/2016a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a`` ``7.49.1`` ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``7.52.1`` ``gimkl/2017a``, ``intel/2016b`` ``7.53.1`` ``GCCcore/6.3.0`` ``7.54.0`` ``GCCcore/6.3.0`` ``7.55.1`` ``GCCcore/6.4.0`` ``7.56.0`` ``GCCcore/6.4.0`` ``7.56.1`` ``GCCcore/6.4.0`` ``7.58.0`` ``GCCcore/6.4.0`` ``7.59.0`` ``GCCcore/6.4.0`` ``7.60.0`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``7.63.0`` ``GCCcore/8.2.0`` ``7.66.0`` ``GCCcore/8.3.0`` ========== =================================================================================== .. _list_software_custodian_970: *custodian* +++++++++++ A simple JIT job management framework in Python. *homepage*: https://pypi.python.org/pypi/custodian ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.1.0`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== .. _list_software_cutadapt_854: *cutadapt* ++++++++++ Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads. *homepage*: http://opensource.scilifelab.se/projects/cutadapt/ ========= ================== ================================================ version versionsuffix toolchain ========= ================== ================================================ ``1.9.1`` ``-Python-2.7.11`` ``foss/2016a`` ``1.9.1`` ``-Python-2.7.12`` ``foss/2016b`` ``1.14`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` ``1.15`` ``-Python-3.5.2`` ``foss/2016b`` ``1.16`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``1.16`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.16`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.18`` ``GCCcore/8.2.0`` ``1.18`` ``-Python-2.7.15`` ``foss/2018b`` ``1.18`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``2.1`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================== ================================================ .. _list_software_CVS_236: *CVS* +++++ CVS is a version control system, an important component of Source Configuration Management (SCM). *homepage*: https://savannah.nongnu.org/projects/cvs =========== =================================================== version toolchain =========== =================================================== ``1.11.23`` ``GCC/4.8.2``, ``GCCcore/4.9.3``, ``GCCcore/6.4.0`` =========== =================================================== .. _list_software_CVXOPT_484: *CVXOPT* ++++++++ CVXOPT is a free software package for convex optimization based on the Python programming language. Its main purpose is to make the development of software for convex optimization applications straightforward by building on Python's extensive standard library and on the strengths of Python as a high-level programming language. *homepage*: http://cvxopt.org ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.1.9`` ``-Python-2.7.13`` ``intel/2017a`` ``1.2.1`` ``-Python-3.6.4`` ``intel/2018a`` ``1.2.3`` ``foss/2019a`` ========= ================== =============== .. _list_software_CVXPY_410: *CVXPY* +++++++ CVXPY is a Python-embedded modeling language for convex optimization problems. It allows you to express your problem in a natural way that follows the math, rather than in the restrictive standard form required by solvers. *homepage*: https://www.cvxpy.org/ ========== ============== version toolchain ========== ============== ``1.0.24`` ``foss/2019a`` ========== ============== .. _list_software_cysignals_973: *cysignals* +++++++++++ The cysignals package provides mechanisms to handle interrupts (and other signals and errors) in Cython code. *homepage*: https://pypi.org/project/cysignals/ ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``1.10.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.10.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ========== ================== =============================== .. _list_software_Cython_629: *Cython* ++++++++ The Cython language makes writing C extensions for the Python language as easy as Python itself. Cython is a source code translator based on the well-known Pyrex, but supports more cutting edge functionality and optimizations. *homepage*: https://pypi.python.org/pypi/Cython/ =========== ================== =============================== version versionsuffix toolchain =========== ================== =============================== ``0.23.4`` ``-Python-2.7.10`` ``gimkl/2.11.5`` ``0.24.1`` ``-Python-2.7.11`` ``foss/2016a`` ``0.25.2`` ``-Python-2.7.12`` ``foss/2016b`` ``0.25.2`` ``-Python-3.6.4`` ``intel/2018a`` ``0.27.3`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``0.29.10`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``0.29.10`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` =========== ================== =============================== .. _list_software_cytoolz_788: *cytoolz* +++++++++ Cython implementation of the toolz package, which provides high performance utility functions for iterables, functions, and dictionaries. *homepage*: https://github.com/pytoolz/cytoolz ========== ================= ================= version versionsuffix toolchain ========== ================= ================= ``0.10.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================= ================= .. _list_software_cytosim_776: *cytosim* +++++++++ Cytosim is a cytoskeleton simulation engine written in C++ working on Mac OS, GNU/Linux and Windows (with Cygwin). *homepage*: https://github.com/nedelec/cytosim ============ ============= =============== version versionsuffix toolchain ============ ============= =============== ``20190117`` ``-mkl`` ``gomkl/2019a`` ============ ============= =============== .. _list_software_cyvcf2_589: *cyvcf2* ++++++++ cython + htslib == fast VCF and BCF processing *homepage*: https://github.com/brentp/cyvcf2 =========== ================= =============================== version versionsuffix toolchain =========== ================= =============================== ``0.10.10`` ``-Python-3.6.6`` ``foss/2018b`` ``0.11.5`` ``foss/2019a``, ``intel/2019a`` =========== ================= =============================== .. _list_software_letter_d: *D* --- :ref:`list_software_dadi_402` - :ref:`list_software_dagitty_758` - :ref:`list_software_damageproto_1171` - :ref:`list_software_dammit_636` - :ref:`list_software_DANPOS2_503` - :ref:`list_software_DAS_Tool_725` - :ref:`list_software_dask_419` - :ref:`list_software_datamash_835` - :ref:`list_software_davix_540` - :ref:`list_software_DB_134` - :ref:`list_software_DB_File_613` - :ref:`list_software_DBD-mysql_813` - :ref:`list_software_DBG2OLC_477` - :ref:`list_software_DBus_366` - :ref:`list_software_dbus-glib_889` - :ref:`list_software_dcm2niix_798` - :ref:`list_software_DCMTK_371` - :ref:`list_software_deal.II_598` - :ref:`list_software_deap_410` - :ref:`list_software_deconf_623` - :ref:`list_software_DeconICA_694` - :ref:`list_software_deepdiff_823` - :ref:`list_software_DeepSurv_814` - :ref:`list_software_deepTools_943` - :ref:`list_software_Delly_506` - :ref:`list_software_DeMixT_555` - :ref:`list_software_DendroPy_805` - :ref:`list_software_destiny_768` - :ref:`list_software_detonate_852` - :ref:`list_software_DFT-D3_386` - :ref:`list_software_DFTB+_331` - :ref:`list_software_DIAL_282` - :ref:`list_software_DIAMOND_508` - :ref:`list_software_DicomBrowser_1232` - :ref:`list_software_Diffutils_938` - :ref:`list_software_dill_421` - :ref:`list_software_distributed_1187` - :ref:`list_software_DL_POLY_Classic_1364` - :ref:`list_software_DMTCP_376` - :ref:`list_software_DOLFIN_444` - :ref:`list_software_Doris_513` - :ref:`list_software_dotNET-Core-Runtime_1781` - :ref:`list_software_double-conversion_1774` - :ref:`list_software_Doxygen_734` - :ref:`list_software_Drake_487` - :ref:`list_software_dropEst_737` - :ref:`list_software_DSA_216` - :ref:`list_software_DSRC_300` - :ref:`list_software_Dsuite_622` - :ref:`list_software_dtcmp_536` - :ref:`list_software_dxpy_453` .. _list_software_dadi_402: *dadi* ++++++ ∂a∂i implements methods for demographic history and selection inference from genetic data, based on diffusion approximations to the allele frequency spectrum. *homepage*: https://bitbucket.org/gutenkunstlab/dadi ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.7.0`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== .. _list_software_dagitty_758: *dagitty* +++++++++ A port of the web-based software 'DAGitty', available at , for analyzing structural causal models (also known as directed acyclic graphs or DAGs). This package computes covariate adjustment sets for estimating causal effects, enumerates instrumental variables, derives testable implications (d-separation and vanishing tetrads), generates equivalent models, and includes a simple facility for data simulation. *homepage*: https://cran.r-project.org/web/packages/dagitty/ ========= ============= ============== version versionsuffix toolchain ========= ============= ============== ``0.2-2`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== .. _list_software_damageproto_1171: *damageproto* +++++++++++++ X protocol and ancillary headers for xinerama *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== version toolchain ========= =============================== ``1.2.1`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_dammit_636: *dammit* ++++++++ dammit is a simple de novo transcriptome annotator. It was born out of the observations that annotation is mundane and annoying, all the individual pieces of the process exist already, and the existing solutions are overly complicated or rely on crappy non-free software. *homepage*: http://www.camillescott.org/dammit/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.3.2`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== .. _list_software_DANPOS2_503: *DANPOS2* +++++++++ A toolkit for Dynamic Analysis of Nucleosome and Protein Occupancy by Sequencing, version 2 *homepage*: https://sites.google.com/site/danposdoc ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.2.2`` ``-Python-2.7.12`` ``foss/2016b`` ========= ================== ============== .. _list_software_DAS_Tool_725: *DAS_Tool* ++++++++++ DAS Tool is an automated method that integrates the results of a flexible number of binning algorithms to calculate an optimized, non-redundant set of bins from a single assembly. *homepage*: https://github.com/cmks/DAS_Tool ========= ========================== ============== version versionsuffix toolchain ========= ========================== ============== ``1.1.1`` ``-R-3.5.1-Python-2.7.15`` ``foss/2018b`` ========= ========================== ============== .. _list_software_dask_419: *dask* ++++++ Dask natively scales Python. Dask provides advanced parallelism for analytics, enabling performance at scale for the tools you love. *homepage*: https://dask.org/ ========== ================== =================================================== version versionsuffix toolchain ========== ================== =================================================== ``0.8.2`` ``-Python-2.7.11`` ``intel/2016a`` ``0.8.2`` ``-Python-3.5.1`` ``intel/2016a`` ``0.11.0`` ``-Python-2.7.11`` ``foss/2016a`` ``0.11.0`` ``-Python-2.7.12`` ``intel/2016b`` ``0.11.0`` ``-Python-3.5.2`` ``intel/2016b`` ``0.12.0`` ``-Python-2.7.12`` ``intel/2016b`` ``0.12.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` ``0.16.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``0.16.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``0.17.0`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` ``0.17.0`` ``-Python-3.6.1`` ``intel/2017a`` ``0.17.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``0.19.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``1.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.1.4`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``2.3.0`` ``-Python-3.7.2`` ``foss/2019a`` ``2.8.0`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================== =================================================== .. _list_software_datamash_835: *datamash* ++++++++++ GNU datamash performs basic numeric, textual and statistical operations on input data files *homepage*: https://www.gnu.org/software/datamash/ ======= ============== version toolchain ======= ============== ``1.3`` ``foss/2018a`` ======= ============== .. _list_software_davix_540: *davix* +++++++ The davix project aims to make file management over HTTP-based protocols simple. The focus is on high-performance remote I/O and data management of large collections of files. Currently, there is support for the WebDav (link is external), Amazon S3 (link is external), Microsoft Azure (link is external), and HTTP (link is external) protocols. *homepage*: http://dmc.web.cern.ch/projects/davix/home ========= =============== version toolchain ========= =============== ``0.6.6`` ``intel/2017a`` ========= =============== .. _list_software_DB_134: *DB* ++++ Berkeley DB enables the development of custom data management solutions, without the overhead traditionally associated with such custom projects. *homepage*: http://www.oracle.com/technetwork/products/berkeleydb =========== ================================== version toolchain =========== ================================== ``4.8.30`` ``intel/2016a`` ``6.2.23`` ``foss/2016a`` ``6.2.32`` ``GCCcore/6.4.0``, ``intel/2017a`` ``18.1.25`` ``GCCcore/7.3.0`` ``18.1.32`` ``GCCcore/8.2.0`` =========== ================================== .. _list_software_DB_File_613: *DB_File* +++++++++ Perl5 access to Berkeley DB version 1.x. *homepage*: http://perldoc.perl.org/DB_File.html ========= ================ =============== version versionsuffix toolchain ========= ================ =============== ``1.835`` ``-Perl-5.20.3`` ``intel/2016a`` ``1.835`` ``-Perl-5.22.1`` ``foss/2016a`` ========= ================ =============== .. _list_software_DBD-mysql_813: *DBD-mysql* +++++++++++ Perl binding for MySQL *homepage*: https://metacpan.org/pod/distribution/DBD-mysql/lib/DBD/mysql.pm ========= ================ =============================== version versionsuffix toolchain ========= ================ =============================== ``4.032`` ``-Perl-5.22.2`` ``intel/2016a`` ``4.033`` ``-Perl-5.24.0`` ``intel/2016b`` ``4.042`` ``-Perl-5.24.1`` ``intel/2017a`` ``4.046`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``4.046`` ``-Perl-5.26.1`` ``intel/2018a`` ``4.048`` ``-Perl-5.28.0`` ``foss/2018b`` ``4.050`` ``-Perl-5.28.1`` ``foss/2019a`` ========= ================ =============================== .. _list_software_DBG2OLC_477: *DBG2OLC* +++++++++ DBG2OLC:Efficient Assembly of Large Genomes Using Long Erroneous Reads of the Third Generation Sequencing Technologies *homepage*: https://github.com/yechengxi/DBG2OLC ============ ========================================================== version toolchain ============ ========================================================== ``20170208`` ``intel/2016b``, ``intel/2017a`` ``20180221`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ============ ========================================================== .. _list_software_DBus_366: *DBus* ++++++ D-Bus is a message bus system, a simple way for applications to talk to one another. In addition to interprocess communication, D-Bus helps coordinate process lifecycle; it makes it simple and reliable to code a "single instance" application or daemon, and to launch applications and daemons on demand when their services are needed. *homepage*: http://dbus.freedesktop.org/ =========== ==================================== version toolchain =========== ==================================== ``1.10.8`` ``foss/2016a``, ``intel/2016a`` ``1.10.12`` ``intel/2016b`` ``1.10.20`` ``GCCcore/6.4.0`` ``1.11.20`` ``intel/2017a`` ``1.13.0`` ``intel/2017b`` ``1.13.6`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.13.8`` ``GCCcore/8.2.0`` ``1.13.12`` ``GCCcore/8.3.0`` =========== ==================================== .. _list_software_dbus-glib_889: *dbus-glib* +++++++++++ D-Bus is a message bus system, a simple way for applications to talk to one another. *homepage*: http://dbus.freedesktop.org/doc/dbus-glib ========= ===================================================== version toolchain ========= ===================================================== ``0.106`` ``foss/2016a``, ``intel/2016a`` ``0.108`` ``intel/2016b``, ``intel/2017a`` ``0.110`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``intel/2017b`` ========= ===================================================== .. _list_software_dcm2niix_798: *dcm2niix* ++++++++++ dcm2niix is a designed to convert neuroimaging data from the DICOM format to the NIfTI format. *homepage*: https://github.com/rordenlab/dcm2niix ================ ==================================== version toolchain ================ ==================================== ``1.0.20180622`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.0.20190902`` ``GCCcore/7.3.0`` ================ ==================================== .. _list_software_DCMTK_371: *DCMTK* +++++++ DCMTK is a collection of libraries and applications implementing large parts the DICOM standard. It includes software for examining, constructing and converting DICOM image files, handling offline media, sending and receiving images over a network connection, as well as demonstrative image storage and worklist servers. *homepage*: https://dicom.offis.de/dcmtk ========= ================= version toolchain ========= ================= ``3.6.3`` ``GCCcore/7.3.0`` ``3.6.5`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_deal.II_598: *deal.II* +++++++++ deal.II is a C++ program library targeted at the computational solution of partial differential equations using adaptive finite elements. *homepage*: https://www.dealii.org ========= =============== version toolchain ========= =============== ``9.1.1`` ``intel/2019a`` ========= =============== .. _list_software_deap_410: *deap* ++++++ DEAP is a novel evolutionary computation framework for rapid prototyping and testing of ideas. It seeks to make algorithms explicit and data structures transparent. *homepage*: http://deap.readthedocs.org/en/master/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.9.2`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== .. _list_software_deconf_623: *deconf* ++++++++ decomposition (deconfounding) of OMICS datasets in heterogeneous tissues *homepage*: http://web.cbio.uct.ac.za/~renaud/CRAN/ ========= ============= ============== version versionsuffix toolchain ========= ============= ============== ``1.0.1`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== .. _list_software_DeconICA_694: *DeconICA* ++++++++++ Deconvolution of transcriptome through Immune Component Analysis (DeconICA) is an R package for identifying immune-related signals in transcriptome through deconvolution or unsupervised source separation methods. *homepage*: https://urszulaczerwinska.github.io/DeconICA ========= ============= ============== version versionsuffix toolchain ========= ============= ============== ``0.1.0`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== .. _list_software_deepdiff_823: *deepdiff* ++++++++++ DeepDiff: Deep Difference of dictionaries, iterables and almost any other object recursively. *homepage*: https://deepdiff.readthedocs.io/en/latest/ ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``3.3.0`` ``-Python-2.7.15`` ``intel/2018b`` ``3.3.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``4.0.6`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========= ================== =============================== .. _list_software_DeepSurv_814: *DeepSurv* ++++++++++ DeepSurv is a deep learning approach to survival analysis. *homepage*: https://github.com/jaredleekatzman/DeepSurv ================== ================= ================== version versionsuffix toolchain ================== ================= ================== ``2.0.0-20180922`` ``-Python-3.6.6`` ``fosscuda/2018b`` ================== ================= ================== .. _list_software_deepTools_943: *deepTools* +++++++++++ deepTools is a suite of python tools particularly developed for the efficient analysis of high-throughput sequencing data, such as ChIP-seq, RNA-seq or MNase-seq. *homepage*: https://deeptools.readthedocs.io/ ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``2.5.4`` ``-Python-3.6.3`` ``intel/2017b`` ``3.3.1`` ``-Python-3.6.6`` ``foss/2018b`` ``3.3.1`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================= =============== .. _list_software_Delly_506: *Delly* +++++++ Delly is an integrated structural variant (SV) prediction method that can discover, genotype and visualize deletions, tandem duplications, inversions and translocations at single-nucleotide resolution in short-read massively parallel sequencing data. *homepage*: https://github.com/dellytools/delly ========= ================= ========== version versionsuffix toolchain ========= ================= ========== ``0.7.8`` ``-linux_x86_64`` ``system`` ========= ================= ========== .. _list_software_DeMixT_555: *DeMixT* ++++++++ Cell type-specific deconvolution of heterogeneous tumor samples with two or three components using expression data from RNAseq or microarray platforms. *homepage*: https://bioinformatics.mdanderson.org/main/DeMixT ========= ============= ============== version versionsuffix toolchain ========= ============= ============== ``0.2.1`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== .. _list_software_DendroPy_805: *DendroPy* ++++++++++ A Python library for phylogenetics and phylogenetic computing: reading, writing, simulation, processing and manipulation of phylogenetic trees (phylogenies) and characters. *homepage*: https://pypi.python.org/pypi/DendroPy/ ========= ================== ================================== version versionsuffix toolchain ========= ================== ================================== ``4.4.0`` ``GCCcore/8.2.0``, ``intel/2019a`` ``4.4.0`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== ================================== .. _list_software_destiny_768: *destiny* +++++++++ R packages to create and plot diffusion maps. *homepage*: https://bioconductor.org/packages/destiny ========= ============= =============== version versionsuffix toolchain ========= ============= =============== ``2.5.6`` ``-R-3.4.0`` ``intel/2017a`` ========= ============= =============== .. _list_software_detonate_852: *detonate* ++++++++++ DETONATE (DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation) consists of two component packages, RSEM-EVAL and REF-EVAL. Both packages are mainly intended to be used to evaluate de novo transcriptome assemblies, although REF-EVAL can be used to compare sets of any kinds of genomic sequences. *homepage*: http://deweylab.biostat.wisc.edu/detonate/ ======== =============== version toolchain ======== =============== ``1.11`` ``intel/2017b`` ======== =============== .. _list_software_DFT-D3_386: *DFT-D3* ++++++++ DFT-D3 implements a dispersion correction for density functionals, Hartree-Fock and semi-empirical quantum chemical methods. *homepage*: http://www.thch.uni-bonn.de/tc/index.php?section=downloads&subsection=DFT-D3&lang=english ========= =============== version toolchain ========= =============== ``3.2.0`` ``intel/2019a`` ========= =============== .. _list_software_DFTB+_331: *DFTB+* +++++++ DFTB+ is a fast and efficient versatile quantum mechanical simulation package. It is based on the Density Functional Tight Binding (DFTB) method, containing almost all of the useful extensions which have been developed for the DFTB framework so far. Using DFTB+ you can carry out quantum mechanical simulations like with ab-initio density functional theory based packages, but in an approximate way gaining typically around two order of magnitude in speed. *homepage*: https://www.dftb-plus.info ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.3.1`` ``intel/2017a`` ``17.1`` ``-Python-2.7.14`` ``intel/2017b`` ========= ================== =============== .. _list_software_DIAL_282: *DIAL* ++++++ DIAL (De novo Identification of Alleles) is a collection of programs to automate the discovery of alleles for a species where we lack a reference sequence. The SNPs/alleles are specifically selected for a low error rate in genotyping assays. *homepage*: http://www.bx.psu.edu/miller_lab/ ============== ============== version toolchain ============== ============== ``2011.06.06`` ``foss/2016a`` ============== ============== .. _list_software_DIAMOND_508: *DIAMOND* +++++++++ DIAMOND is a sequence aligner for protein and translated DNA searches, designed for high performance analysis of big sequence data. *homepage*: https://github.com/bbuchfink/diamond ========== ================================================================ version toolchain ========== ================================================================ ``0.9.22`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` ``0.9.24`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ========== ================================================================ .. _list_software_DicomBrowser_1232: *DicomBrowser* ++++++++++++++ DicomBrowser is an application for inspecting and modifying DICOM metadata in many files at once. *homepage*: http://nrg.wustl.edu/software/dicom-browser/ =========== ================== ========== version versionsuffix toolchain =========== ================== ========== ``1.7.0b5`` ``-Java-1.7.0_80`` ``system`` =========== ================== ========== .. _list_software_Diffutils_938: *Diffutils* +++++++++++ Diffutils: GNU diff utilities - find the differences between files *homepage*: http://www.gnu.org/software/diffutils/diffutils.html ======= ============= version toolchain ======= ============= ``3.3`` ``GCC/4.8.2`` ======= ============= .. _list_software_dill_421: *dill* ++++++ dill extends python's pickle module for serializing and de-serializing python objects to the majority of the built-in python types. Serialization is the process of converting an object to a byte stream, and the inverse of which is converting a byte stream back to on python object hierarchy. *homepage*: https://pypi.org/project/dill/ ========= ================= version toolchain ========= ================= ``0.3.0`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_distributed_1187: *distributed* +++++++++++++ Dask.distributed is a lightweight library for distributed computing in Python. It extends both the concurrent.futures and dask APIs to moderate sized clusters. *homepage*: https://distributed.readthedocs.io/ ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``1.14.3`` ``-Python-2.7.12`` ``intel/2016b`` ``1.14.3`` ``-Python-3.5.2`` ``intel/2016b`` ``1.21.6`` ``-Python-3.6.4`` ``intel/2018a`` ========== ================== =============== .. _list_software_DL_POLY_Classic_1364: *DL_POLY_Classic* +++++++++++++++++ DL_POLY Classic is a freely available molecular dynamics program developed from the DL_POLY_2 package. This version does not install the java gui. *homepage*: http://ccpforge.cse.rl.ac.uk/gf/project/dl_poly_classic/ ======== ================= =============================== version versionsuffix toolchain ======== ================= =============================== ``1.9`` ``intel/2016b`` ``1.9`` ``-PLUMED-2.2.3`` ``intel/2016b`` ``1.10`` ``foss/2019b``, ``intel/2019b`` ======== ================= =============================== .. _list_software_DMTCP_376: *DMTCP* +++++++ DMTCP is a tool to transparently checkpoint the state of multiple simultaneous applications, including multi-threaded and distributed applications. It operates directly on the user binary executable, without any Linux kernel modules or other kernel modifications. *homepage*: https://github.com/dmtcp/dmtcp ========= ============================== version toolchain ========= ============================== ``2.4.5`` ``system`` ``2.5.0`` ``foss/2016a`` ``2.5.1`` ``system`` ``2.5.2`` ``foss/2016b``, ``foss/2018b`` ========= ============================== .. _list_software_DOLFIN_444: *DOLFIN* ++++++++ DOLFIN is the C++/Python interface of FEniCS, providing a consistent PSE (Problem Solving Environment) for ordinary and partial differential equations. *homepage*: https://bitbucket.org/fenics-project/dolfin ================== ================= ============== version versionsuffix toolchain ================== ================= ============== ``2018.1.0.post1`` ``-Python-3.6.4`` ``foss/2018a`` ================== ================= ============== .. _list_software_Doris_513: *Doris* +++++++ Delft object-oriented radar interferometric software *homepage*: http://doris.tudelft.nl/ ============= =============================== version toolchain ============= =============================== ``4.02`` ``intel/2017a`` ``4.04beta4`` ``foss/2018a``, ``intel/2017a`` ``4.06beta2`` ``intel/2017a`` ============= =============================== .. _list_software_dotNET-Core-Runtime_1781: *dotNET-Core-Runtime* +++++++++++++++++++++ .NET is a free, cross-platform, open source developer platform for building many different types of applications. *homepage*: https://www.microsoft.com/net/ ========= ================= version toolchain ========= ================= ``2.0.7`` ``GCCcore/6.4.0`` ========= ================= .. _list_software_double-conversion_1774: *double-conversion* +++++++++++++++++++ Efficient binary-decimal and decimal-binary conversion routines for IEEE doubles. *homepage*: https://github.com/google/double-conversion ========= ==================================== version toolchain ========= ==================================== ``3.0.3`` ``foss/2018a`` ``3.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ==================================== .. _list_software_Doxygen_734: *Doxygen* +++++++++ Doxygen is a documentation system for C++, C, Java, Objective-C, Python, IDL (Corba and Microsoft flavors), Fortran, VHDL, PHP, C#, and to some extent D. *homepage*: http://www.doxygen.org =========== ======================================================================================================================================================= version toolchain =========== ======================================================================================================================================================= ``1.8.9.1`` ``GCC/4.9.2`` ``1.8.10`` ``GNU/4.9.3-2.25``, ``intel/2016.02-GCC-4.9`` ``1.8.11`` ``GCC/4.9.2``, ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``1.8.13`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``gimkl/2017a`` ``1.8.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``1.8.15`` ``GCCcore/8.2.0`` ``1.8.16`` ``GCCcore/8.3.0`` =========== ======================================================================================================================================================= .. _list_software_Drake_487: *Drake* +++++++ Drake is a simple-to-use, extensible, text-based data workflow tool that organizes command execution around data and its dependencies. *homepage*: https://github.com/Factual/drake ========= ============= ========== version versionsuffix toolchain ========= ============= ========== ``1.0.3`` ``-Java-1.8`` ``system`` ========= ============= ========== .. _list_software_dropEst_737: *dropEst* +++++++++ Pipeline for initial analysis of droplet-based single-cell RNA-seq data *homepage*: https://github.com/hms-dbmi/dropEst ========= ============= =============== version versionsuffix toolchain ========= ============= =============== ``0.7.1`` ``-R-3.4.3`` ``intel/2017b`` ========= ============= =============== .. _list_software_DSA_216: *DSA* +++++ Digital Sorting Algorithm *homepage*: https://github.com/zhandong/DSA ======= ============= ============== version versionsuffix toolchain ======= ============= ============== ``1.0`` ``-R-3.5.1`` ``foss/2018b`` ======= ============= ============== .. _list_software_DSRC_300: *DSRC* ++++++ DNA Sequence Reads Compression is an application designed for compression of data files containing reads from DNA sequencing in FASTQ format. The amount of such files can be huge, e.g., a few (or tens) of gigabytes, so a need for a robust data compression tool is clear. Usually universal compression programs like gzip or bzip2 are used for this purpose, but it is obvious that a specialized tool can work better. *homepage*: http://sun.aei.polsl.pl/dsrc ========= ================= ========== version versionsuffix toolchain ========= ================= ========== ``2.0rc`` ``-linux-64-bit`` ``system`` ========= ================= ========== .. _list_software_Dsuite_622: *Dsuite* ++++++++ Fast calculation of the ABBA-BABA statistics across many populations/species *homepage*: https://github.com/millanek/Dsuite ============ ======================================== version toolchain ============ ======================================== ``20190713`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ============ ======================================== .. _list_software_dtcmp_536: *dtcmp* +++++++ Datatype Compare (DTCMP) Library for sorting and ranking distributed data using MPI *homepage*: https://github.com/llnl/dtcmp ========= ================================ version toolchain ========= ================================ ``1.1.0`` ``gompi/2019a``, ``iimpi/2019a`` ========= ================================ .. _list_software_dxpy_453: *dxpy* ++++++ DNAnexus Platform API bindings for Python *homepage*: http://autodoc.dnanexus.com/ =========== ================== =============== version versionsuffix toolchain =========== ================== =============== ``0.266.1`` ``-Python-2.7.14`` ``intel/2018a`` =========== ================== =============== .. _list_software_letter_e: *E* --- :ref:`list_software_ea-utils_804` - :ref:`list_software_earthengine-api_1521` - :ref:`list_software_EasyBuild_898` - :ref:`list_software_EasyQC_550` - :ref:`list_software_ecCodes_694` - :ref:`list_software_ED2_187` - :ref:`list_software_EggLib_554` - :ref:`list_software_eggnog-mapper_1321` - :ref:`list_software_Eigen_488` - :ref:`list_software_EIGENSOFT_676` - :ref:`list_software_elastix_762` - :ref:`list_software_Elk_284` - :ref:`list_software_ELPA_290` - :ref:`list_software_ELPH_297` - :ref:`list_software_Emacs_489` - :ref:`list_software_EMAN2_339` - :ref:`list_software_EMBOSS_457` - :ref:`list_software_emcee_511` - :ref:`list_software_enaBrowserTool_1462` - :ref:`list_software_enchant_737` - :ref:`list_software_entrypoints_1231` - :ref:`list_software_EPD_217` - :ref:`list_software_EPIC_289` - :ref:`list_software_EricScript_1016` - :ref:`list_software_ESMF_299` - :ref:`list_software_Essentia_828` - :ref:`list_software_ETE_222` - :ref:`list_software_ETSF_IO_553` - :ref:`list_software_eudev_537` - :ref:`list_software_EvidentialGene_1412` - :ref:`list_software_evmix_553` - :ref:`list_software_ExaBayes_786` - :ref:`list_software_Exonerate_939` - :ref:`list_software_expat_546` - :ref:`list_software_expect_649` - :ref:`list_software_eXpress_746` - :ref:`list_software_Extrae_617` .. _list_software_ea-utils_804: *ea-utils* ++++++++++ Command-line tools for processing biological sequencing data. Barcode demultiplexing, adapter trimming, etc. Primarily written to support an Illumina based pipeline - but should work with any FASTQs. *homepage*: http://expressionanalysis.github.io/ea-utils/ ============ =============================================== version toolchain ============ =============================================== ``1.04.807`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ============ =============================================== .. _list_software_earthengine-api_1521: *earthengine-api* +++++++++++++++++ Python and JavaScript bindings for calling the Earth Engine API *homepage*: https://github.com/google/earthengine-api =========== ================== =============== version versionsuffix toolchain =========== ================== =============== ``0.1.143`` ``-Python-2.7.14`` ``intel/2018a`` =========== ================== =============== .. _list_software_EasyBuild_898: *EasyBuild* +++++++++++ EasyBuild is a software build and installation framework written in Python that allows you to install software in a structured, repeatable and robust way. *homepage*: https://easybuilders.github.io/easybuild ========== ========== version toolchain ========== ========== ``1.0.0`` ``system`` ``1.0.1`` ``system`` ``1.0.2`` ``system`` ``1.1.0`` ``system`` ``1.2.0`` ``system`` ``1.3.0`` ``system`` ``1.4.0`` ``system`` ``1.5.0`` ``system`` ``1.6.0`` ``system`` ``1.7.0`` ``system`` ``1.8.0`` ``system`` ``1.8.1`` ``system`` ``1.8.2`` ``system`` ``1.9.0`` ``system`` ``1.10.0`` ``system`` ``1.11.0`` ``system`` ``1.11.1`` ``system`` ``1.12.0`` ``system`` ``1.12.1`` ``system`` ``1.13.0`` ``system`` ``1.14.0`` ``system`` ``1.15.0`` ``system`` ``1.15.1`` ``system`` ``1.15.2`` ``system`` ``1.16.0`` ``system`` ``1.16.1`` ``system`` ``1.16.2`` ``system`` ``2.0.0`` ``system`` ``2.1.0`` ``system`` ``2.1.1`` ``system`` ``2.2.0`` ``system`` ``2.3.0`` ``system`` ``2.4.0`` ``system`` ``2.5.0`` ``system`` ``2.6.0`` ``system`` ``2.7.0`` ``system`` ``2.8.0`` ``system`` ``2.8.1`` ``system`` ``2.8.2`` ``system`` ``2.9.0`` ``system`` ``3.0.0`` ``system`` ``3.0.1`` ``system`` ``3.0.2`` ``system`` ``3.1.0`` ``system`` ``3.1.1`` ``system`` ``3.1.2`` ``system`` ``3.2.0`` ``system`` ``3.2.1`` ``system`` ``3.3.0`` ``system`` ``3.3.1`` ``system`` ``3.4.0`` ``system`` ``3.4.1`` ``system`` ``3.5.0`` ``system`` ``3.5.1`` ``system`` ``3.5.2`` ``system`` ``3.5.3`` ``system`` ``3.6.0`` ``system`` ``3.6.1`` ``system`` ``3.6.2`` ``system`` ``3.7.0`` ``system`` ``3.7.1`` ``system`` ``3.8.0`` ``system`` ``3.8.1`` ``system`` ``3.9.0`` ``system`` ``3.9.1`` ``system`` ``3.9.2`` ``system`` ``3.9.3`` ``system`` ``3.9.4`` ``system`` ``4.0.0`` ``system`` ``4.0.1`` ``system`` ``4.1.0`` ``system`` ========== ========== .. _list_software_EasyQC_550: *EasyQC* ++++++++ EasyQC is an R-package that provides advanced functionality to (1) perform file-level QC of single genome-wide association (GWA) data-sets (2) conduct quality control across several GWA data-sets (meta-level QC) (3) simplify data-handling of large-scale GWA data-sets. *homepage*: http://www.uni-regensburg.de/medizin/epidemiologie-praeventivmedizin/genetische-epidemiologie/software/ ======= ============= =============== version versionsuffix toolchain ======= ============= =============== ``9.2`` ``-R-3.3.1`` ``intel/2016b`` ======= ============= =============== .. _list_software_ecCodes_694: *ecCodes* +++++++++ ecCodes is a package developed by ECMWF which provides an application programming interface and a set of tools for decoding and encoding messages in the following formats: WMO FM-92 GRIB edition 1 and edition 2, WMO FM-94 BUFR edition 3 and edition 4, WMO GTS abbreviated header (only decoding). *homepage*: https://software.ecmwf.int/wiki/display/ECC/ecCodes+Home ========== ================================ version toolchain ========== ================================ ``2.7.3`` ``intel/2018a`` ``2.8.2`` ``intel/2018a`` ``2.9.2`` ``intel/2018b``, ``iomkl/2018b`` ``2.12.5`` ``gompi/2019a`` ``2.15.0`` ``iimpi/2019b`` ========== ================================ .. _list_software_ED2_187: *ED2* +++++ The Ecosystem Demography Biosphere Model (ED2) is an integrated terrestrial biosphere model incorporating hydrology, land-surface biophysics, vegetation dynamics, and soil carbon and nitrogen biogeochemistry *homepage*: https://github.com/EDmodel/ED2 ============ ============= =============== version versionsuffix toolchain ============ ============= =============== ``20170201`` ``intel/2017a`` ``20170201`` ``-serial`` ``intel/2017a`` ============ ============= =============== .. _list_software_EggLib_554: *EggLib* ++++++++ EggLib is a C++/Python library and program package for evolutionary genetics and genomics. *homepage*: http://egglib.sourceforge.net/ ========== =============== version toolchain ========== =============== ``2.1.10`` ``intel/2016a`` ========== =============== .. _list_software_eggnog-mapper_1321: *eggnog-mapper* +++++++++++++++ eggnog-mapper is a tool for fast functional annotation of novel sequences (genes or proteins) using precomputed eggNOG-based orthology assignments *homepage*: http://eggnog-mapper.embl.de ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.0.3`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============== .. _list_software_Eigen_488: *Eigen* +++++++ Eigen is a C++ template library for linear algebra: matrices, vectors, numerical solvers, and related algorithms. *homepage*: http://eigen.tuxfamily.org/index.php?title=Main_Page ========== =========================================== version toolchain ========== =========================================== ``3.2.3`` ``foss/2016a``, ``foss/2016b`` ``3.2.5`` ``system`` ``3.2.6`` ``system`` ``3.2.7`` ``foss/2016a``, ``intel/2016a`` ``3.2.8`` ``foss/2016a``, ``intel/2016a``, ``system`` ``3.2.9`` ``foss/2016b``, ``intel/2016b`` ``3.2.10`` ``intel/2016b`` ``3.3.2`` ``foss/2016b``, ``intel/2016b`` ``3.3.3`` ``GCCcore/6.3.0``, ``intel/2016b`` ``3.3.4`` ``system`` ``3.3.5`` ``system`` ``3.3.7`` ``system`` ========== =========================================== .. _list_software_EIGENSOFT_676: *EIGENSOFT* +++++++++++ The EIGENSOFT package combines functionality from our population genetics methods (Patterson et al. 2006) and our EIGENSTRAT stratification correction method (Price et al. 2006). The EIGENSTRAT method uses principal components analysis to explicitly model ancestry differences between cases and controls along continuous axes of variation; the resulting correction is specific to a candidate marker’s variation in frequency across ancestral populations, minimizing spurious associations while maximizing power to detect true associations. The EIGENSOFT package has a built-in plotting script and supports multiple file formats and quantitative phenotypes. *homepage*: http://www.hsph.harvard.edu/alkes-price/software/ ========= =============================== version toolchain ========= =============================== ``6.0.1`` ``foss/2016a`` ``6.1.1`` ``foss/2016a`` ``6.1.4`` ``foss/2016b`` ``7.2.1`` ``foss/2019a``, ``intel/2019a`` ========= =============================== .. _list_software_elastix_762: *elastix* +++++++++ elastix: a toolbox for rigid and nonrigid registration of images. *homepage*: http://elastix.isi.uu.nl/ ========= ============== version toolchain ========= ============== ``4.9.0`` ``foss/2018a`` ========= ============== .. _list_software_Elk_284: *Elk* +++++ An all-electron full-potential linearised augmented-plane wave (FP-LAPW) code with many advanced features. Written originally at Karl-Franzens-Universität Graz as a milestone of the EXCITING EU Research and Training Network, the code is designed to be as simple as possible so that new developments in the field of density functional theory (DFT) can be added quickly and reliably. *homepage*: http://elk.sourceforge.net/ ========== =============== version toolchain ========== =============== ``4.0.15`` ``intel/2016b`` ``4.3.6`` ``intel/2017a`` ========== =============== .. _list_software_ELPA_290: *ELPA* ++++++ Eigenvalue SoLvers for Petaflop-Applications . *homepage*: http://elpa.rzg.mpg.de =================== ================================================ version toolchain =================== ================================================ ``2015.02.002`` ``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` ``2016.05.004`` ``intel/2016b``, ``intel/2017a`` ``2016.11.001.pre`` ``foss/2018b``, ``intel/2018b`` ``2017.11.001`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b`` ``2018.05.001`` ``foss/2018b``, ``intel/2018b`` ``2018.11.001`` ``intel/2019a`` =================== ================================================ .. _list_software_ELPH_297: *ELPH* ++++++ ELPH is a general-purpose Gibbs sampler for finding motifs in a set of DNA or protein sequences. The program takes as input a set containing anywhere from a few dozen to thousands of sequences, and searches through them for the most common motif, assuming that each sequence contains one copy of the motif. We have used ELPH to find patterns such as ribosome binding sites (RBSs) and exon splicing enhancers (ESEs). *homepage*: http://ccb.jhu.edu/software/ELPH/index.shtml ========= ============== version toolchain ========= ============== ``1.0.1`` ``foss/2018b`` ========= ============== .. _list_software_Emacs_489: *Emacs* +++++++ GNU Emacs is an extensible, customizable text editor--and more. At its core is an interpreter for Emacs Lisp, a dialect of the Lisp programming language with extensions to support text editing. *homepage*: http://www.gnu.org/software/emacs/ ======== ============= ======================================================= version versionsuffix toolchain ======== ============= ======================================================= ``24.3`` ``GCC/4.8.3`` ``24.3`` ``-bare`` ``GCC/4.8.3`` ``24.4`` ``GCC/4.9.2`` ``24.5`` ``GCC/4.9.3-2.25`` ``25.1`` ``foss/2016a`` ``25.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ======== ============= ======================================================= .. _list_software_EMAN2_339: *EMAN2* +++++++ EMAN2 is a broadly based greyscale scientific image processing suite with a primary focus on processing data from transmission electron microscopes. *homepage*: https://blake.bcm.edu/emanwiki/EMAN2 ========= =============================== ================================== version versionsuffix toolchain ========= =============================== ================================== ``2.3`` ``system`` ``2.3`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a`` ``2.21a`` ``-Python-2.7.14-Boost-1.63.0`` ``foss/2018a`` ========= =============================== ================================== .. _list_software_EMBOSS_457: *EMBOSS* ++++++++ EMBOSS is 'The European Molecular Biology Open Software Suite'. EMBOSS is a free Open Source software analysis package specially developed for the needs of the molecular biology (e.g. EMBnet) user community. *homepage*: http://emboss.sourceforge.net/ ========= ================= ================================================================================================================================ version versionsuffix toolchain ========= ================= ================================================================================================================================ ``6.6.0`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a``, ``intel/2018b`` ``6.6.0`` ``-X11-20170314`` ``intel/2017a`` ========= ================= ================================================================================================================================ .. _list_software_emcee_511: *emcee* +++++++ Emcee is an extensible, pure-Python implementation of Goodman & Weare's Affine Invariant Markov chain Monte Carlo (MCMC) Ensemble sampler. It's designed for Bayesian parameter estimation and it's really sweet! *homepage*: https://dfm.io/emcee ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``2.2.1`` ``foss/2019a`` ``2.2.1`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.2.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ========= ================== =============================== .. _list_software_enaBrowserTool_1462: *enaBrowserTool* ++++++++++++++++ enaBrowserTools is a set of scripts that interface with the ENA web services to download data from ENA easily, without any knowledge of scripting required. *homepage*: https://github.com/enasequence/enaBrowserTools/ ========= ================= ================= version versionsuffix toolchain ========= ================= ================= ``1.5.4`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========= ================= ================= .. _list_software_enchant_737: *enchant* +++++++++ Enchant is a library (and command-line program) that wraps a number of different spelling libraries and programs with a consistent interface. *homepage*: https://abiword.github.io/enchant/ ========= =============== version toolchain ========= =============== ``1.6.1`` ``intel/2017a`` ========= =============== .. _list_software_entrypoints_1231: *entrypoints* +++++++++++++ Entry points are a way for Python packages to advertise objects with some common interface. *homepage*: https://github.com/takluyver/entrypoints ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``0.2.2`` ``-Python-2.7.11`` ``foss/2016a`` ``0.2.2`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``0.2.2`` ``-Python-3.5.1`` ``foss/2016a`` ``0.2.2`` ``-Python-3.5.2`` ``intel/2016b`` ========= ================== =============================== .. _list_software_EPD_217: *EPD* +++++ The Enthought Python Distribution provides scientists with a comprehensive set of tools to perform rigorous data analysis and visualization. Python, distinguished by its flexibility, coherence, and ease-of-use, is rapidly becoming the programming language of choice for researchers worldwide. EPD extends this capacity with a powerful collection of Python libraries to enable interactive technical computing and cross-platform rapid application development. *homepage*: http://www.enthought.com/products/edudownload.php ============= ========== version toolchain ============= ========== ``7.3-2-rh5`` ``system`` ============= ========== .. _list_software_EPIC_289: *EPIC* ++++++ Package implementing EPIC method to estimate the proportion of immune, stromal, endothelial and cancer or other cells from bulk gene expression data. *homepage*: https://gfellerlab.shinyapps.io/EPIC_1-1 ======= ============= ============== version versionsuffix toolchain ======= ============= ============== ``1.1`` ``-R-3.5.1`` ``foss/2018b`` ======= ============= ============== .. _list_software_EricScript_1016: *EricScript* ++++++++++++ EricScript is a computational framework for the discovery of gene fusions in paired end RNA-seq data. *homepage*: https://sites.google.com/site/bioericscript/home ========= ============= =============== version versionsuffix toolchain ========= ============= =============== ``0.5.5`` ``-R-3.4.0`` ``intel/2017a`` ========= ============= =============== .. _list_software_ESMF_299: *ESMF* ++++++ The Earth System Modeling Framework (ESMF) is software for building and coupling weather, climate, and related models. *homepage*: https://sourceforge.net/projects/esmf ============ ================ ================================================================= version versionsuffix toolchain ============ ================ ================================================================= ``6.3.0rp1`` ``intel/2017a`` ``6.3.0rp1`` ``-HDF5-1.8.18`` ``intel/2017a`` ``7.0.0`` ``foss/2016a`` ``7.0.2`` ``intel/2017b`` ``7.1.0r`` ``foss/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``8.0.0`` ``intel/2019b`` ============ ================ ================================================================= .. _list_software_Essentia_828: *Essentia* ++++++++++ Open-source library and tools for audio and music analysis, description and synthesis *homepage*: https://essentia.upf.edu ============= ================== ============== version versionsuffix toolchain ============= ================== ============== ``2.1_beta5`` ``-Python-2.7.15`` ``foss/2019a`` ============= ================== ============== .. _list_software_ETE_222: *ETE* +++++ A Python framework for the analysis and visualization of trees *homepage*: http://etetoolkit.org ============ ================== =============== version versionsuffix toolchain ============ ================== =============== ``3.0.0b36`` ``-Python-2.7.12`` ``intel/2016b`` ============ ================== =============== .. _list_software_ETSF_IO_553: *ETSF_IO* +++++++++ A library of F90 routines to read/write the ETSF file format has been written. It is called ETSF_IO and available under LGPL. *homepage*: http://www.etsf.eu/resources/software/libraries_and_tools ========= ================================================================================================= version toolchain ========= ================================================================================================= ``1.0.4`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ========= ================================================================================================= .. _list_software_eudev_537: *eudev* +++++++ eudev is a fork of systemd-udev with the goal of obtaining better compatibility with existing software such as OpenRC and Upstart, older kernels, various toolchains and anything else required by users and various distributions. *homepage*: https://wiki.gentoo.org/wiki/Project:Eudev ========= ================================================= version toolchain ========= ================================================= ``3.1.5`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``3.2`` ``GCCcore/4.9.3`` ``3.2.2`` ``GCCcore/6.4.0`` ========= ================================================= .. _list_software_EvidentialGene_1412: *EvidentialGene* ++++++++++++++++ EvidentialGene is a genome informatics project for "Evidence Directed Gene Construction for Eukaryotes", for constructing high quality, accurate gene sets for animals and plants (any eukaryotes), being developed by Don Gilbert at Indiana University, gilbertd at indiana edu. *homepage*: http://arthropods.eugenes.org/EvidentialGene/ ============== ================ =============== version versionsuffix toolchain ============== ================ =============== ``2018.01.01`` ``-Perl-5.24.1`` ``intel/2017a`` ============== ================ =============== .. _list_software_evmix_553: *evmix* +++++++ evmix: Extreme Value Mixture Modelling, Threshold Estimation and Boundary Corrected Kernel Density Estimation *homepage*: http://cran.r-project.org/web/packages/evmix ======= ============= =============== version versionsuffix toolchain ======= ============= =============== ``2.6`` ``-R-3.3.1`` ``intel/2016b`` ======= ============= =============== .. _list_software_ExaBayes_786: *ExaBayes* ++++++++++ ExaBayes is a software package for Bayesian tree inference. It is particularly suitable for large-scale analyses on computer clusters *homepage*: https://cme.h-its.org/exelixis/web/software/exabayes/ ======= ============== version toolchain ======= ============== ``1.5`` ``foss/2016b`` ======= ============== .. _list_software_Exonerate_939: *Exonerate* +++++++++++ Exonerate is a generic tool for pairwise sequence comparison. It allows you to align sequences using a many alignment models, using either exhaustive dynamic programming, or a variety of heuristics. *homepage*: https://www.ebi.ac.uk/about/vertebrate-genomics/software/exonerate ========= ==================================================================================================================================================================== version toolchain ========= ==================================================================================================================================================================== ``2.4.0`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a`` ========= ==================================================================================================================================================================== .. _list_software_expat_546: *expat* +++++++ Expat is an XML parser library written in C. It is a stream-oriented parser in which an application registers handlers for things the parser might find in the XML document (like start tags) *homepage*: https://libexpat.github.io ========= ========================================================================================================================= version toolchain ========= ========================================================================================================================= ``2.1.0`` ``GCC/4.9.2``, ``foss/2016a``, ``intel/2016a`` ``2.1.1`` ``foss/2016a``, ``intel/2016a`` ``2.2.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` ``2.2.4`` ``GCCcore/6.4.0`` ``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.2.6`` ``GCCcore/8.2.0`` ``2.2.7`` ``GCCcore/8.3.0`` ========= ========================================================================================================================= .. _list_software_expect_649: *expect* ++++++++ Expect is a tool for automating interactive applications such as telnet, ftp, passwd, fsck, rlogin, tip, etc. Expect really makes this stuff trivial. Expect is also useful for testing these same applications. *homepage*: https://core.tcl.tk/expect/index ========== ================= version toolchain ========== ================= ``5.45.4`` ``GCCcore/7.3.0`` ========== ================= .. _list_software_eXpress_746: *eXpress* +++++++++ Streaming quantification for high-throughput sequencing *homepage*: https://pachterlab.github.io/eXpress ========= =============== version toolchain ========= =============== ``1.5.1`` ``intel/2017b`` ========= =============== .. _list_software_Extrae_617: *Extrae* ++++++++ Extrae is the core instrumentation package developed by the Performance Tools group at BSC. Extrae is capable of instrumenting applications based on MPI, OpenMP, pthreads, CUDA1, OpenCL1, and StarSs1 using different instrumentation approaches. The information gathered by Extrae typically includes timestamped events of runtime calls, performance counters and source code references. Besides, Extrae provides its own API to allow the user to manually instrument his or her application. *homepage*: http://www.bsc.es/computer-sciences/performance-tools ========= =============== version toolchain ========= =============== ``3.4.1`` ``foss/2017a`` ``3.7.1`` ``intel/2019a`` ========= =============== .. _list_software_letter_f: *F* --- :ref:`list_software_f90cache_707` - :ref:`list_software_Faber_480` - :ref:`list_software_faceswap_842` - :ref:`list_software_FALCON_435` - :ref:`list_software_FANN_291` - :ref:`list_software_fast5_483` - :ref:`list_software_FASTA_367` - :ref:`list_software_FastaIndex_999` - :ref:`list_software_FastANI_614` - :ref:`list_software_FastME_544` - :ref:`list_software_fastp_542` - :ref:`list_software_fastPHASE_799` - :ref:`list_software_fastq-tools_1149` - :ref:`list_software_FastQ_Screen_1182` - :ref:`list_software_FastQC_546` - :ref:`list_software_FastQTL_639` - :ref:`list_software_fastqz_665` - :ref:`list_software_FastRFS_633` - :ref:`list_software_fastStructure_1407` - :ref:`list_software_FastTree_798` - :ref:`list_software_FASTX-Toolkit_1177` - :ref:`list_software_fatslim_752` - :ref:`list_software_fbm_309` - :ref:`list_software_FCM_214` - :ref:`list_software_FDS_221` - :ref:`list_software_fdstools_878` - :ref:`list_software_FDTD_Solutions_1361` - :ref:`list_software_feh_307` - :ref:`list_software_Ferret_616` - :ref:`list_software_FFC_207` - :ref:`list_software_FFLAS-FFPACK_836` - :ref:`list_software_FFmpeg_565` - :ref:`list_software_ffnet_531` - :ref:`list_software_FFTW_311` - :ref:`list_software_FGSL_300` - :ref:`list_software_FIAT_292` - :ref:`list_software_Fiji_386` - :ref:`list_software_file_416` - :ref:`list_software_Filtlong_831` - :ref:`list_software_find_circ_929` - :ref:`list_software_findhap_730` - :ref:`list_software_findutils_978` - :ref:`list_software_fineRADstructure_1642` - :ref:`list_software_fineSTRUCTURE_1139` - :ref:`list_software_Firefox_723` - :ref:`list_software_FireWorks_924` - :ref:`list_software_fixesproto_1107` - :ref:`list_software_FLANN_367` - :ref:`list_software_FLASH_366` - :ref:`list_software_Flask_497` - :ref:`list_software_FLEUR_382` - :ref:`list_software_flex_431` - :ref:`list_software_FlexiDot_799` - :ref:`list_software_FLINT_381` - :ref:`list_software_FLTK_305` - :ref:`list_software_FLUENT_462` - :ref:`list_software_Flye_400` - :ref:`list_software_FMILibrary_945` - :ref:`list_software_FMRIprep_741` - :ref:`list_software_fmt_327` - :ref:`list_software_FoldX_477` - :ref:`list_software_fontconfig_1069` - :ref:`list_software_fontsproto_1118` - :ref:`list_software_foss_443` - :ref:`list_software_fosscuda_856` - :ref:`list_software_FoX_269` - :ref:`list_software_FPM_227` - :ref:`list_software_fqtrim_659` - :ref:`list_software_fqzcomp_768` - :ref:`list_software_FragGeneScan_1156` - :ref:`list_software_FRANz_417` - :ref:`list_software_FreeFem++_752` - :ref:`list_software_freeglut_862` - :ref:`list_software_FreeImage_869` - :ref:`list_software_FreeSurfer_1017` - :ref:`list_software_freetype_868` - :ref:`list_software_FreeXL_550` - :ref:`list_software_FriBidi_665` - :ref:`list_software_FSL_229` - :ref:`list_software_FSLeyes_667` - :ref:`list_software_FTGL_301` - :ref:`list_software_fullrmc_757` - :ref:`list_software_FUNWAVE-TVD_823` - :ref:`list_software_FUSE_307` - :ref:`list_software_future_667` - :ref:`list_software_fxtract_764` .. _list_software_f90cache_707: *f90cache* ++++++++++ f90cache is a compiler cache. It acts as a caching pre-processor to Fortran compilers, using the -E compiler switch and a hash to detect when a compilation can be satisfied from cache. This often results in a great speedup in common compilations. *homepage*: http://people.irisa.fr/Edouard.Canot/f90cache/ ======== ========== version toolchain ======== ========== ``0.96`` ``system`` ======== ========== .. _list_software_Faber_480: *Faber* +++++++ Faber started as a clone of Boost.Build, to experiment with a new Python frontend. Meanwhile it has evolved into a new build system, which retains most of the features found in Boost.Build, but with (hopefully !) much simplified logic, in addition of course to using Python as scripting language, rather than Jam. The original bjam engine is still in use as scheduler, though at this point that is mostly an implementation detail. *homepage*: https://stefanseefeld.github.io/faber ======= ================= version toolchain ======= ================= ``0.3`` ``GCCcore/8.3.0`` ======= ================= .. _list_software_faceswap_842: *faceswap* ++++++++++ Faceswap is a tool that utilizes deep learning to recognize and swap faces in pictures and videos. *homepage*: https://github.com/deepfakes/faceswap ============ ================= ============== version versionsuffix toolchain ============ ================= ============== ``20180212`` ``-Python-3.6.3`` ``foss/2017b`` ============ ================= ============== .. _list_software_FALCON_435: *FALCON* ++++++++ Falcon: a set of tools for fast aligning long reads for consensus and assembly *homepage*: https://github.com/PacificBiosciences/FALCON ========= =============== version toolchain ========= =============== ``1.8.8`` ``intel/2017b`` ========= =============== .. _list_software_FANN_291: *FANN* ++++++ Fast Artificial Neural Network Library is a free open source neural network library, which implements multilayer artificial neural networks in C with support for both fully connected and sparsely connected networks. *homepage*: http://leenissen.dk ========= ================================== version toolchain ========= ================================== ``2.2.0`` ``GCCcore/6.4.0``, ``intel/2018a`` ========= ================================== .. _list_software_fast5_483: *fast5* +++++++ A lightweight C++ library for accessing Oxford Nanopore Technologies sequencing data. *homepage*: http://simpsonlab.github.io/2017/02/27/packing_fast5/ ========= ========== version toolchain ========= ========== ``0.6.5`` ``system`` ========= ========== .. _list_software_FASTA_367: *FASTA* +++++++ The FASTA programs find regions of local or global (new) similarity between protein or DNA sequences, either by searching Protein or DNA databases, or by identifying local duplications within a sequence. *homepage*: http://fasta.bioch.virginia.edu =========== ============== version toolchain =========== ============== ``36.3.5e`` ``foss/2016b`` =========== ============== .. _list_software_FastaIndex_999: *FastaIndex* ++++++++++++ FastA index (.fai) handler compatible with samtools faidx *homepage*: https://github.com/lpryszcz/FastaIndex =========== ================== =============== version versionsuffix toolchain =========== ================== =============== ``0.11rc7`` ``-Python-2.7.14`` ``intel/2017b`` =========== ================== =============== .. _list_software_FastANI_614: *FastANI* +++++++++ FastANI is developed for fast alignment-free computation of whole-genome Average Nucleotide Identity (ANI). ANI is defined as mean nucleotide identity of orthologous gene pairs shared between two microbial genomes. FastANI supports pairwise comparison of both complete and draft genome assemblies. *homepage*: https://www.iodbc.org/ ======= ============================================================== version toolchain ======= ============================================================== ``1.1`` ``foss/2018b``, ``intel/2018b`` ``1.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ======= ============================================================== .. _list_software_FastME_544: *FastME* ++++++++ FastME: a comprehensive, accurate and fast distance-based phylogeny inference program. *homepage*: http://www.atgc-montpellier.fr/fastme/ =========== ================================ version toolchain =========== ================================ ``2.1.5`` ``foss/2016a`` ``2.1.6.1`` ``intel/2018a``, ``intel/2018b`` =========== ================================ .. _list_software_fastp_542: *fastp* +++++++ A tool designed to provide fast all-in-one preprocessing for FastQ files. This tool is developed in C++ with multithreading supported to afford high performance. *homepage*: https://github.com/OpenGene/fastp ========== ============================================= version toolchain ========== ============================================= ``0.19.7`` ``foss/2018b`` ``0.20.0`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.5.281`` ========== ============================================= .. _list_software_fastPHASE_799: *fastPHASE* +++++++++++ fastPHASE: software for haplotype reconstruction, and estimating missing genotypes from population data Documentation: http://scheet.org/code/fastphase_doc_1.4.pdf *homepage*: http://stephenslab.uchicago.edu/software.html#fastphase ========= ========== version toolchain ========= ========== ``1.4.8`` ``system`` ========= ========== .. _list_software_fastq-tools_1149: *fastq-tools* +++++++++++++ This package provides a number of small and efficient programs to perform common tasks with high throughput sequencing data in the FASTQ format. All of the programs work with typical FASTQ files as well as gzipped FASTQ files. *homepage*: https://homes.cs.washington.edu/~dcjones/fastq-tools/ ======= ============================== version toolchain ======= ============================== ``0.8`` ``foss/2016b``, ``foss/2018b`` ======= ============================== .. _list_software_FastQ_Screen_1182: *FastQ_Screen* ++++++++++++++ FastQ Screen allows you to screen a library of sequences in FastQ format against a set of sequence databases so you can see if the composition of the library matches with what you expect. *homepage*: http://www.bioinformatics.babraham.ac.uk/projects/fastq_screen/ ========== ================ =============== version versionsuffix toolchain ========== ================ =============== ``0.11.3`` ``-Perl-5.24.0`` ``foss/2016b`` ``0.11.4`` ``-Perl-5.24.0`` ``foss/2016b`` ``0.12.0`` ``-Perl-5.26.1`` ``intel/2018a`` ``0.13.0`` ``-Perl-5.28.0`` ``foss/2018b`` ========== ================ =============== .. _list_software_FastQC_546: *FastQC* ++++++++ FastQC is a quality control application for high throughput sequence data. It reads in sequence data in a variety of formats and can either provide an interactive application to review the results of several different QC checks, or create an HTML based report which can be integrated into a pipeline. *homepage*: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ ========== =================== ========== version versionsuffix toolchain ========== =================== ========== ``0.10.1`` ``-Java-1.7.0_80`` ``system`` ``0.11.2`` ``-Java-1.7.0_60`` ``system`` ``0.11.3`` ``-Java-1.7.0_80`` ``system`` ``0.11.4`` ``-Java-1.8.0_66`` ``system`` ``0.11.4`` ``-Java-1.8.0_74`` ``system`` ``0.11.5`` ``-Java-1.7.0_80`` ``system`` ``0.11.5`` ``-Java-1.8.0_144`` ``system`` ``0.11.5`` ``-Java-1.8.0_74`` ``system`` ``0.11.7`` ``-Java-1.8.0_162`` ``system`` ``0.11.8`` ``-Java-1.8`` ``system`` ``0.11.8`` ``-Java-11`` ``system`` ========== =================== ========== .. _list_software_FastQTL_639: *FastQTL* +++++++++ FastQTL is a QTL mapper *homepage*: http://fastqtl.sourceforge.net/ ========= ============== version toolchain ========= ============== ``2.184`` ``foss/2018b`` ========= ============== .. _list_software_fastqz_665: *fastqz* ++++++++ fastqz is a compressor for FASTQ files. FASTQ is the output of DNA sequencing machines. It is one of the compressors described in the paper: Bonfield JK, Mahoney MV (2013) Compression of FASTQ and SAM Format Sequencing Data. (mirror) PLoS ONE 8(3): e59190. doi:10.1371/journal.pone.0059190 *homepage*: http://mattmahoney.net/dc/fastqz/ ======= ============= version toolchain ======= ============= ``1.5`` ``GCC/4.8.2`` ======= ============= .. _list_software_FastRFS_633: *FastRFS* +++++++++ Fast Robinson Foulds Supertrees *homepage*: https://github.com/pranjalv123/FastRFS ================ =============== version toolchain ================ =============== ``1.0-20190613`` ``gompi/2019a`` ================ =============== .. _list_software_fastStructure_1407: *fastStructure* +++++++++++++++ fastStructure is a fast algorithm for inferring population structure from large SNP genotype data. It is based on a variational Bayesian framework for posterior inference and is written in Python2.x. *homepage*: https://rajanil.github.io/fastStructure/ ======= ================== ============== version versionsuffix toolchain ======= ================== ============== ``1.0`` ``-Python-2.7.11`` ``foss/2016a`` ``1.0`` ``-Python-2.7.12`` ``foss/2016b`` ``1.0`` ``-Python-2.7.13`` ``foss/2017a`` ``1.0`` ``-Python-2.7.15`` ``foss/2019a`` ======= ================== ============== .. _list_software_FastTree_798: *FastTree* ++++++++++ FastTree infers approximately-maximum-likelihood phylogenetic trees from alignments of nucleotide or protein sequences. FastTree can handle alignments with up to a million of sequences in a reasonable amount of time and memory. *homepage*: http://www.microbesonline.org/fasttree/ ========== ================================================================= version toolchain ========== ================================================================= ``2.1.10`` ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ``2.1.11`` ``GCCcore/8.2.0`` ========== ================================================================= .. _list_software_FASTX-Toolkit_1177: *FASTX-Toolkit* +++++++++++++++ The FASTX-Toolkit is a collection of command line tools for Short-Reads FASTA/FASTQ files preprocessing. *homepage*: http://hannonlab.cshl.edu/fastx_toolkit/ ========== ================================================================== version toolchain ========== ================================================================== ``0.0.14`` ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2018a`` ========== ================================================================== .. _list_software_fatslim_752: *fatslim* +++++++++ FATSLiM stands for “Fast Analysis Toolbox for Simulations of Lipid Membranes” and its goal is to provide an efficient, yet robust, tool to extract physical parameters from MD trajectories. *homepage*: https://github.com/FATSLiM/fatslim ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``0.2.1`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================= ============== .. _list_software_fbm_309: *fbm* +++++ Exact methods for simulating fractional Brownian motion and fractional Gaussian noise in Python *homepage*: https://pypi.org/project/fbm ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``0.2.0`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== .. _list_software_FCM_214: *FCM* +++++ FCM is a set of tools for managing and building source code. *homepage*: http://www.metoffice.gov.uk/research/collaboration/fcm ========= ========== version toolchain ========= ========== ``2.3.1`` ``system`` ========= ========== .. _list_software_FDS_221: *FDS* +++++ Fire Dynamics Simulator (FDS) is a large-eddy simulation (LES) code for low-speed flows, with an emphasis on smoke and heat transport from fires. *homepage*: https://pages.nist.gov/fds-smv/ ========= ============= ================================ version versionsuffix toolchain ========= ============= ================================ ``6.0.1`` ``-no-OFED`` ``system`` ``6.5.2`` ``intel/2016b`` ``6.5.3`` ``intel/2017a`` ``6.6.0`` ``intel/2017b``, ``intel/2018a`` ``6.7.0`` ``intel/2018a`` ========= ============= ================================ .. _list_software_fdstools_878: *fdstools* ++++++++++ Forensic DNA Sequencing Tools Tools for characterisation and filtering of PCR stutter artefacts and other systemic noise in Next Generation Sequencing data of forensic STR markers. *homepage*: https://git.lumc.nl/jerryhoogenboom/fdstools ============ ================== ============== version versionsuffix toolchain ============ ================== ============== ``20160322`` ``-Python-2.7.11`` ``foss/2016a`` ============ ================== ============== .. _list_software_FDTD_Solutions_1361: *FDTD_Solutions* ++++++++++++++++ High performance FDTD-method Maxwell solver for the design, analysis and optimization of nanophotonic devices, processes and materials. *homepage*: http://www.lumerical.com/tcad-products/fdtd/ ============= ========== version toolchain ============= ========== ``8.6.2`` ``system`` ``8.11.337`` ``system`` ``8.16.982`` ``system`` ``8.20.1731`` ``system`` ============= ========== .. _list_software_feh_307: *feh* +++++ feh is an X11 image viewer aimed mostly at console users. Unlike most other viewers, it does not have a fancy GUI, but simply displays images. It is controlled via commandline arguments and configurable key/mouse actions. *homepage*: https://feh.finalrewind.org/ ======== ================= version toolchain ======== ================= ``2.26`` ``GCCcore/6.4.0`` ======== ================= .. _list_software_Ferret_616: *Ferret* ++++++++ Ferret is an interactive computer visualization and analysis environment designed to meet the needs of oceanographers and meteorologists analyzing large and complex gridded data sets. *homepage*: http://ferret.pmel.noaa.gov/ ======= =============== version toolchain ======= =============== ``7.3`` ``intel/2017b`` ======= =============== .. _list_software_FFC_207: *FFC* +++++ The FEniCS Form Compiler (FFC) is a compiler for finite element variational forms. *homepage*: https://bitbucket.org/fenics-project/ffc ============ ================= ============== version versionsuffix toolchain ============ ================= ============== ``2018.1.0`` ``-Python-3.6.4`` ``foss/2018a`` ============ ================= ============== .. _list_software_FFLAS-FFPACK_836: *FFLAS-FFPACK* ++++++++++++++ Finite Field Linear Algebra Subroutines / Package *homepage*: https://linbox-team.github.io/fflas-ffpack/ ========= ============== version toolchain ========= ============== ``2.2.0`` ``foss/2016a`` ========= ============== .. _list_software_FFmpeg_565: *FFmpeg* ++++++++ A complete, cross-platform solution to record, convert and stream audio and video. *homepage*: https://www.ffmpeg.org/ =========== =================================================== version toolchain =========== =================================================== ``0.10.16`` ``gimkl/2.11.5``, ``intel/2016a`` ``2.8.6`` ``intel/2016a`` ``2.8.7`` ``foss/2016a``, ``intel/2016a`` ``3.0.2`` ``foss/2016a``, ``intel/2016a`` ``3.1.3`` ``foss/2016b``, ``intel/2016b`` ``3.2.4`` ``gimkl/2017a`` ``3.3.1`` ``foss/2016b`` ``3.3.4`` ``intel/2017a`` ``3.4`` ``GCCcore/6.4.0`` ``3.4.1`` ``foss/2017b``, ``intel/2017b`` ``3.4.2`` ``foss/2018a``, ``intel/2018a`` ``3.4.5`` ``foss/2018b`` ``4.0`` ``foss/2018a``, ``intel/2018a`` ``4.0.1`` ``intel/2018a`` ``4.1`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``4.1.3`` ``GCCcore/8.2.0`` ``4.2.1`` ``GCCcore/8.3.0`` =========== =================================================== .. _list_software_ffnet_531: *ffnet* +++++++ Feed-forward neural network solution for python *homepage*: http://ffnet.sourceforge.net/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.8.3`` ``-Python-2.7.11`` ``intel/2016a`` ========= ================== =============== .. _list_software_FFTW_311: *FFTW* ++++++ FFTW is a C subroutine library for computing the discrete Fourier transform (DFT) in one or more dimensions, of arbitrary input size, and of both real and complex data. *homepage*: http://www.fftw.org ========= ============= ============================================================================================================================================================================================== version versionsuffix toolchain ========= ============= ============================================================================================================================================================================================== ``2.1.5`` ``intel/2016b``, ``intel/2017a``, ``intel/2018b`` ``3.3.4`` ``gmpich/2016a``, ``gmvapich2/1.7.20``, ``gmvapich2/2016a``, ``gompi/2016.04``, ``gompi/2016.06``, ``gompi/2016.07``, ``gompi/2016a``, ``gompi/2016b``, ``intel/2016a``, ``intel/2016b`` ``3.3.5`` ``gompi/2016.07``, ``gompi/2016.09``, ``gompi/2016b``, ``intel/2016b`` ``3.3.6`` ``gimpi/2017b``, ``gimpic/2017b``, ``gompi/2017a``, ``gompi/2017b``, ``gompic/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` ``3.3.7`` ``gimkl/2017a``, ``gimpi/2018a``, ``gmpich/2017.08``, ``gompi/2018a``, ``gompic/2018a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``iomkl/2018a`` ``3.3.7`` ``-serial`` ``GCC/6.4.0-2.28`` ``3.3.8`` ``gompi/2018.08``, ``gompi/2018b``, ``gompi/2019a``, ``gompi/2019b``, ``gompic/2018b``, ``gompic/2019a``, ``gompic/2019b``, ``intel/2018b``, ``intel/2019a``, ``intel/2019b``, ``iomkl/2018b`` ========= ============= ============================================================================================================================================================================================== .. _list_software_FGSL_300: *FGSL* ++++++ FGSL: A Fortran interface to the GNU Scientific Library *homepage*: https://www.lrz.de/services/software/mathematik/gsl/fortran/ ========= =============== version toolchain ========= =============== ``1.1.0`` ``intel/2016b`` ========= =============== .. _list_software_FIAT_292: *FIAT* ++++++ The FInite element Automatic Tabulator (FIAT) supports generation of arbitrary order instances of the Lagrange elements on lines, triangles, and tetrahedra. It is also capable of generating arbitrary order instances of Jacobi-type quadrature rules on the same element shapes. *homepage*: https://bitbucket.org/fenics-project/fiat ============ ================== =============================== version versionsuffix toolchain ============ ================== =============================== ``1.6.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``2018.1.0`` ``-Python-3.6.4`` ``foss/2018a`` ============ ================== =============================== .. _list_software_Fiji_386: *Fiji* ++++++ Fiji is an image processing package—a 'batteries-included' distribution of ImageJ, bundling a lot of plugins which facilitate scientific image analysis. This release is based on ImageJ 2.0.0-rc-69/1.52p. *homepage*: https://fiji.sc/ ================= ========== version toolchain ================= ========== ``20170530`` ``system`` ``20191119-2057`` ``system`` ================= ========== .. _list_software_file_416: *file* ++++++ The file command is 'a file type guesser', that is, a command-line tool that tells you in words what kind of data a file contains. *homepage*: http://www.darwinsys.com/file/ ======== ================= version toolchain ======== ================= ``5.17`` ``GCC/4.8.2`` ``5.25`` ``intel/2016a`` ``5.28`` ``foss/2016b`` ``5.30`` ``intel/2017a`` ``5.33`` ``GCCcore/6.4.0`` ``5.35`` ``GCCcore/7.3.0`` ======== ================= .. _list_software_Filtlong_831: *Filtlong* ++++++++++ Filtlong is a tool for filtering long reads by quality. It can take a set of long reads and produce a smaller, better subset. It uses both read length (longer is better) and read identity (higher is better) when choosing which reads pass the filter *homepage*: https://github.com/rrwick/Filtlong ========= ============== version toolchain ========= ============== ``0.2.0`` ``foss/2016b`` ========= ============== .. _list_software_find_circ_929: *find_circ* +++++++++++ circRNA detection from RNA-seq reads *homepage*: https://github.com/marvin-jens/find_circ ================ ================== =============== version versionsuffix toolchain ================ ================== =============== ``1.2-20170228`` ``-Python-2.7.14`` ``intel/2017b`` ================ ================== =============== .. _list_software_findhap_730: *findhap* +++++++++ Find haplotypes and impute genotypes using multiple chip sets and sequence data *homepage*: http://aipl.arsusda.gov/software/findhap/ ======= ========== version toolchain ======= ========== ``4`` ``system`` ======= ========== .. _list_software_findutils_978: *findutils* +++++++++++ findutils: The GNU find, locate, updatedb, and xargs utilities *homepage*: http://www.gnu.org/software/findutils/findutils.html ========= ============= version toolchain ========= ============= ``4.4.2`` ``GCC/4.8.2`` ========= ============= .. _list_software_fineRADstructure_1642: *fineRADstructure* ++++++++++++++++++ A package for population structure inference from RAD-seq data *homepage*: http://cichlid.gurdon.cam.ac.uk/fineRADstructure.html ============ =============== version toolchain ============ =============== ``20180709`` ``intel/2018a`` ============ =============== .. _list_software_fineSTRUCTURE_1139: *fineSTRUCTURE* +++++++++++++++ fineSTRUCTURE is a fast and powerful algorithm for identifying population structure using dense sequencing data. *homepage*: https://people.maths.bris.ac.uk/~madjl/finestructure/finestructure_info.html ========= =============== version toolchain ========= =============== ``2.1.3`` ``intel/2017b`` ========= =============== .. _list_software_Firefox_723: *Firefox* +++++++++ Firefox is a free, open source Web browser for Windows, Linux and Mac OS X. It is based on the Mozilla code base and offers customization options and features such as its capability to block pop-up windows, tabbed browsing, privacy and security measures, smart searching, and RSS live bookmarks. *homepage*: https://www.mozilla.org/en-US/firefox/new/ ========== ========== version toolchain ========== ========== ``44.0.2`` ``system`` ========== ========== .. _list_software_FireWorks_924: *FireWorks* +++++++++++ FireWorks helps run calculation workflows, with a centralized workflow server controlling many worker nodes. *homepage*: https://pypi.python.org/pypi/FireWorks ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.4.2`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== .. _list_software_fixesproto_1107: *fixesproto* ++++++++++++ X.org FixesProto protocol headers. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ======= ================================================= version toolchain ======= ================================================= ``5.0`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ======= ================================================= .. _list_software_FLANN_367: *FLANN* +++++++ FLANN is a library for performing fast approximate nearest neighbor searches in high dimensional spaces. *homepage*: http://www.cs.ubc.ca/research/flann/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.8.4`` ``-Python-2.7.11`` ``intel/2016a`` ``1.8.4`` ``-Python-2.7.14`` ``intel/2017b`` ========= ================== =============== .. _list_software_FLASH_366: *FLASH* +++++++ FLASH (Fast Length Adjustment of SHort reads) is a very fast and accurate software tool to merge paired-end reads from next-generation sequencing experiments. FLASH is designed to merge pairs of reads when the original DNA fragments are shorter than twice the length of reads. The resulting longer reads can significantly improve genome assemblies. They can also improve transcriptome assembly when FLASH is used to merge RNA-seq data. *homepage*: https://ccb.jhu.edu/software/FLASH/ ========== ============================================== version toolchain ========== ============================================== ``1.2.11`` ``foss/2016a``, ``foss/2018a``, ``foss/2018b`` ``2.2.00`` ``foss/2018b`` ========== ============================================== .. _list_software_Flask_497: *Flask* +++++++ " Flask is a lightweight WSGI web application framework. It is designed to make getting started quick and easy, with the ability to scale up to complex applications. *homepage*: https://www.palletsprojects.com/p/flask/ ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``1.0.2`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== .. _list_software_FLEUR_382: *FLEUR* +++++++ FLEUR is a feature-full, freely available FLAPW (full potential linearized augmented planewave) code, based on density-functional theory. *homepage*: http://www.flapw.de/ ========= =============== version toolchain ========= =============== ``0.26e`` ``intel/2016a`` ========= =============== .. _list_software_flex_431: *flex* ++++++ Flex (Fast Lexical Analyzer) is a tool for generating scanners. A scanner, sometimes called a tokenizer, is a program which recognizes lexical patterns in text. *homepage*: http://flex.sourceforge.net/ ========== ================================================================================================================================================================================================================================================================================================================================================= version toolchain ========== ================================================================================================================================================================================================================================================================================================================================================= ``2.5.35`` ``system`` ``2.5.38`` ``GCC/4.8.2`` ``2.5.39`` ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``system`` ``2.6.0`` ``GCC/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``2.6.2`` ``intel/2016b`` ``2.6.3`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/7.1.0``, ``gimkl/2017a``, ``system`` ``2.6.4`` ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/system``, ``system`` ========== ================================================================================================================================================================================================================================================================================================================================================= .. _list_software_FlexiDot_799: *FlexiDot* ++++++++++ Highly customizable, ambiguity-aware dotplots for visual sequence analyses *homepage*: https://github.com/molbio-dresden/flexidot ======== ================== ============== version versionsuffix toolchain ======== ================== ============== ``1.06`` ``-Python-2.7.15`` ``foss/2018b`` ======== ================== ============== .. _list_software_FLINT_381: *FLINT* +++++++ FLINT (Fast Library for Number Theory) is a C library in support of computations in number theory. Operations that can be performed include conversions, arithmetic, computing GCDs, factoring, solving linear systems, and evaluating special functions. In addition, FLINT provides various low-level routines for fast arithmetic. FLINT is extensively documented and tested. *homepage*: http://www.flintlib.org ========= ========================================================== version toolchain ========= ========================================================== ``2.5.2`` ``GCC/7.3.0-2.30``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` ========= ========================================================== .. _list_software_FLTK_305: *FLTK* ++++++ FLTK is a cross-platform C++ GUI toolkit for UNIX/Linux (X11), Microsoft Windows, and MacOS X. FLTK provides modern GUI functionality without the bloat and supports 3D graphics via OpenGL and its built-in GLUT emulation. *homepage*: https://www.fltk.org ========= =================================================================================================================================================================================================== version toolchain ========= =================================================================================================================================================================================================== ``1.3.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.3.4`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b`` ``1.3.5`` ``GCC/8.2.0-2.31.1``, ``GCC/8.3.0`` ========= =================================================================================================================================================================================================== .. _list_software_FLUENT_462: *FLUENT* ++++++++ ANSYS FLUENT software contains the broad physical modeling capabilities needed to model flow, turbulence, heat transfer, and reactions for industrial applications ranging from air flow over an aircraft wing to combustion in a furnace, from bubble columns to oil platforms, from blood flow to semiconductor manufacturing, and from clean room design to wastewater treatment plants. *homepage*: http://www.ansys.com/Products/Simulation+Technology/Fluid+Dynamics/Fluid+Dynamics+Products/ANSYS+Fluent ========== ========== version toolchain ========== ========== ``14.5`` ``system`` ``15.0.7`` ``system`` ``16.0`` ``system`` ``17.1`` ``system`` ``18.0`` ``system`` ``18.1`` ``system`` ========== ========== .. _list_software_Flye_400: *Flye* ++++++ Flye is a de novo assembler for long and noisy reads, such as those produced by PacBio and Oxford Nanopore Technologies. *homepage*: https://github.com/fenderglass/Flye ======= ================== =============== version versionsuffix toolchain ======= ================== =============== ``2.4`` ``-Python-2.7.15`` ``intel/2018b`` ``2.6`` ``-Python-3.7.2`` ``foss/2019a`` ======= ================== =============== .. _list_software_FMILibrary_945: *FMILibrary* ++++++++++++ FMI library is intended as a foundation for applications interfacing FMUs (Functional Mockup Units) that follow FMI Standard. This version of the library supports FMI 1.0 and FMI2.0. See http://www.fmi-standard.org/ *homepage*: https://jmodelica.org/ ========= =============== version toolchain ========= =============== ``2.0.3`` ``intel/2018b`` ========= =============== .. _list_software_FMRIprep_741: *FMRIprep* ++++++++++ FMRIprep is a functional magnetic resonance imaging (fMRI) data preprocessing pipeline that is designed to provide an easily accessible, state-of-the-art interface that is robust to variations in scan acquisition protocols and that requires minimal user input, while providing easily interpretable and comprehensive error and output reporting. *homepage*: https://fmriprep.readthedocs.io ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``1.1.8`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== .. _list_software_fmt_327: *fmt* +++++ fmt (formerly cppformat) is an open-source formatting library. *homepage*: http://fmtlib.net/ ========= ==================================== version toolchain ========= ==================================== ``3.0.1`` ``foss/2016b``, ``intel/2016b`` ``3.0.2`` ``GCCcore/6.4.0``, ``intel/2017a`` ``5.3.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ========= ==================================== .. _list_software_FoldX_477: *FoldX* +++++++ FoldX is used to provide a fast and quantitative estimation of the importance of the interactions contributing to the stability of proteins and protein complexes. *homepage*: http://foldx.crg.es/ =============== ========== version toolchain =============== ========== ``2.5.2`` ``system`` ``3.0-beta5.1`` ``system`` ``3.0-beta6`` ``system`` ``3.0-beta6.1`` ``system`` =============== ========== .. _list_software_fontconfig_1069: *fontconfig* ++++++++++++ Fontconfig is a library designed to provide system-wide font configuration, customization and application access. *homepage*: https://www.freedesktop.org/wiki/Software/fontconfig/ =========== ================== ====================================================================================== version versionsuffix toolchain =========== ================== ====================================================================================== ``2.11.94`` ``foss/2016a``, ``intel/2016a`` ``2.11.95`` ``foss/2016a``, ``intel/2016a`` ``2.12.1`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` ``2.12.1`` ``-libpng-1.6.29`` ``GCCcore/6.3.0`` ``2.12.4`` ``GCCcore/6.4.0`` ``2.12.6`` ``GCCcore/6.4.0`` ``2.13.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.13.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` =========== ================== ====================================================================================== .. _list_software_fontsproto_1118: *fontsproto* ++++++++++++ X11 font extension wire protocol *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= version toolchain ========= ================================================= ``2.1.3`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= .. _list_software_foss_443: *foss* ++++++ GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. *homepage*: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#foss-toolchain =========== ========== version toolchain =========== ========== ``2016.04`` ``system`` ``2016.06`` ``system`` ``2016.07`` ``system`` ``2016.09`` ``system`` ``2016a`` ``system`` ``2016b`` ``system`` ``2017a`` ``system`` ``2017b`` ``system`` ``2018.08`` ``system`` ``2018a`` ``system`` ``2018b`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` =========== ========== .. _list_software_fosscuda_856: *fosscuda* ++++++++++ GCC based compiler toolchain __with CUDA support__, and including OpenMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. *homepage*: (none) ========= ========== version toolchain ========= ========== ``2017b`` ``system`` ``2018a`` ``system`` ``2018b`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` ========= ========== .. _list_software_FoX_269: *FoX* +++++ FoX is an XML library written in Fortran 95. It allows software developers to read, write and modify XML documents from Fortran applications without the complications of dealing with multi-language development. *homepage*: http://homepages.see.leeds.ac.uk/~earawa/FoX/ ========= ================================ version toolchain ========= ================================ ``4.1.2`` ``intel/2017b``, ``intel/2018a`` ========= ================================ .. _list_software_FPM_227: *FPM* +++++ Effing package management! Build packages for multiple platforms (deb, rpm, etc) with great ease and sanity. *homepage*: https://github.com/jordansissel/fpm ========= =============== ========== version versionsuffix toolchain ========= =============== ========== ``1.3.3`` ``-Ruby-2.1.6`` ``system`` ========= =============== ========== .. _list_software_fqtrim_659: *fqtrim* ++++++++ fqtrim is a versatile stand-alone utility that can be used to trim adapters, poly-A tails, terminal unknown bases (Ns) and low quality 3' regions in reads from high-throughput next-generation sequencing machines. *homepage*: http://ccb.jhu.edu/software/fqtrim/ ========= =============== version toolchain ========= =============== ``0.9.4`` ``intel/2016b`` ``0.9.5`` ``intel/2017a`` ========= =============== .. _list_software_fqzcomp_768: *fqzcomp* +++++++++ Fqzcomp is a basic fastq compressor, designed primarily for high performance. Despite that it is comparable to bzip2 for compression levels. *homepage*: http://sourceforge.net/projects/fqzcomp/ ======= ============= version toolchain ======= ============= ``4.6`` ``GCC/4.8.2`` ======= ============= .. _list_software_FragGeneScan_1156: *FragGeneScan* ++++++++++++++ FragGeneScan is an application for finding (fragmented) genes in short reads. *homepage*: http://omics.informatics.indiana.edu/FragGeneScan/ ======== ================================= version toolchain ======== ================================= ``1.31`` ``GCCcore/8.2.0``, ``foss/2018b`` ======== ================================= .. _list_software_FRANz_417: *FRANz* +++++++ A fast and flexible parentage inference program for natural populations. *homepage*: https://www.bioinf.uni-leipzig.de/Software/FRANz ========= ============== version toolchain ========= ============== ``2.0.0`` ``foss/2018a`` ========= ============== .. _list_software_FreeFem++_752: *FreeFem++* +++++++++++ FreeFem++ is a partial differential equation solver. It has its own language. freefem scripts can solve multiphysics non linear systems in 2D and 3D. *homepage*: http://www.freefem.org/ ========== ==================== =============== version versionsuffix toolchain ========== ==================== =============== ``3.58`` ``-downloaded-deps`` ``foss/2017b`` ``3.60`` ``-downloaded-deps`` ``intel/2018a`` ``3.61-1`` ``-downloaded-deps`` ``intel/2018a`` ========== ==================== =============== .. _list_software_freeglut_862: *freeglut* ++++++++++ freeglut is a completely OpenSourced alternative to the OpenGL Utility Toolkit (GLUT) library. *homepage*: http://freeglut.sourceforge.net/ ========= ================ ====================================================================================================================================================================================== version versionsuffix toolchain ========= ================ ====================================================================================================================================================================================== ``3.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` ``3.2.1`` ``GCCcore/8.3.0`` ========= ================ ====================================================================================================================================================================================== .. _list_software_FreeImage_869: *FreeImage* +++++++++++ FreeImage is an Open Source library project for developers who would like to support popular graphics image formats like PNG, BMP, JPEG, TIFF and others as needed by today's multimedia applications. FreeImage is easy to use, fast, multithreading safe. *homepage*: http://freeimage.sourceforge.net ========== ================= version toolchain ========== ================= ``3.18.0`` ``GCCcore/7.3.0`` ========== ================= .. _list_software_FreeSurfer_1017: *FreeSurfer* ++++++++++++ FreeSurfer is a set of tools for analysis and visualization of structural and functional brain imaging data. FreeSurfer contains a fully automatic structural imaging stream for processing cross sectional and longitudinal data. *homepage*: https://surfer.nmr.mgh.harvard.edu/ ========= =================== ========== version versionsuffix toolchain ========= =================== ========== ``5.3.0`` ``-centos4_x86_64`` ``system`` ``5.3.0`` ``-centos6_x86_64`` ``system`` ``6.0.0`` ``-centos6_x86_64`` ``system`` ``6.0.1`` ``-centos6_x86_64`` ``system`` ========= =================== ========== .. _list_software_freetype_868: *freetype* ++++++++++ FreeType 2 is a software font engine that is designed to be small, efficient, highly customizable, and portable while capable of producing high-quality output (glyph images). It can be used in graphics libraries, display servers, font conversion tools, text image generation tools, and many other products as well. *homepage*: http://freetype.org ========== ================== ====================================================================== version versionsuffix toolchain ========== ================== ====================================================================== ``2.6.2`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``2.6.3`` ``foss/2016a``, ``intel/2016a`` ``2.6.5`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` ``2.7`` ``foss/2016b``, ``intel/2016b`` ``2.7.1`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``gimkl/2017a``, ``intel/2016b`` ``2.7.1`` ``-libpng-1.6.29`` ``GCCcore/6.3.0`` ``2.8`` ``GCCcore/6.4.0`` ``2.8.1`` ``GCCcore/6.4.0`` ``2.9`` ``GCCcore/6.4.0`` ``2.9.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.10.1`` ``GCCcore/8.3.0`` ========== ================== ====================================================================== .. _list_software_FreeXL_550: *FreeXL* ++++++++ FreeXL is an open source library to extract valid data from within an Excel (.xls) spreadsheet. *homepage*: https://www.gaia-gis.it/fossil/freexl/index ========= ==================================== version toolchain ========= ==================================== ``1.0.2`` ``foss/2016b``, ``intel/2016b`` ``1.0.3`` ``GCCcore/6.4.0`` ``1.0.5`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ========= ==================================== .. _list_software_FriBidi_665: *FriBidi* +++++++++ The Free Implementation of the Unicode Bidirectional Algorithm. *homepage*: https://github.com/fribidi/fribidi ========= ======================================================= version toolchain ========= ======================================================= ``1.0.1`` ``foss/2018a``, ``intel/2018a`` ``1.0.2`` ``GCCcore/6.4.0`` ``1.0.5`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ======================================================= .. _list_software_FSL_229: *FSL* +++++ FSL is a comprehensive library of analysis tools for FMRI, MRI and DTI brain imaging data. *homepage*: https://www.fmrib.ox.ac.uk/fsl/ ========== ============================== ================================================ version versionsuffix toolchain ========== ============================== ================================================ ``5.0.9`` ``intel/2016a`` ``5.0.9`` ``-Mesa-11.2.1`` ``intel/2016a`` ``5.0.9`` ``-centos6_64`` ``system`` ``5.0.10`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``5.0.11`` ``foss/2018b`` ``5.0.11`` ``-Python-3.6.6`` ``foss/2018b`` ``6.0.1`` ``-Python-2.7.15`` ``foss/2019a`` ``6.0.1`` ``-Python-3.7.2`` ``foss/2019a`` ``6.0.2`` ``-Python-2.7.15`` ``foss/2018b`` ``6.0.2`` ``-Python-2.7.15-CUDA-9.2.88`` ``foss/2018b`` ``6.0.3`` ``-Python-3.7.4`` ``foss/2019b`` ========== ============================== ================================================ .. _list_software_FSLeyes_667: *FSLeyes* +++++++++ FSLeyes is the FSL image viewer. *homepage*: https://git.fmrib.ox.ac.uk/fsl/fsleyes/fsleyes ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``0.15.0`` ``-Python-2.7.13`` ``intel/2017a`` ========== ================== =============== .. _list_software_FTGL_301: *FTGL* ++++++ FTGL is a free open source library to enable developers to use arbitrary fonts in their OpenGL (www.opengl.org) applications. *homepage*: http://ftgl.sourceforge.net/docs/html/ ============= ====================================================================================== version toolchain ============= ====================================================================================== ``2.1.3-rc5`` ``GCCcore/8.2.0``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2018b``, ``intel/2017b`` ============= ====================================================================================== .. _list_software_fullrmc_757: *fullrmc* +++++++++ Reverse Monte Carlo (RMC) is probably best known for its applications in condensed matter physics and solid state chemistry. fullrmc which stands for FUndamental Library Language for Reverse Monte Carlo is different than traditional RMC but a stochastic modelling method to solve an inverse problem whereby an atomic/molecular model is adjusted until its atoms position havei the greatest consistency with a set of experimental data. *homepage*: http://bachiraoun.github.io/fullrmc ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``3.2.0`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============== .. _list_software_FUNWAVE-TVD_823: *FUNWAVE-TVD* +++++++++++++ FUNWAVE–TVD is the TVD version of the fully nonlinear Boussinesq wave model (FUNWAVE) initially developed by Kirby et al. *homepage*: https://fengyanshi.github.io ================ ============= =============== version versionsuffix toolchain ================ ============= =============== ``3.1-20170525`` ``intel/2017a`` ``3.1-20170525`` ``-no-storm`` ``intel/2017a`` ================ ============= =============== .. _list_software_FUSE_307: *FUSE* ++++++ The reference implementation of the Linux FUSE (Filesystem in Userspace) interface *homepage*: https://github.com/libfuse/libfuse ========= =============== version toolchain ========= =============== ``3.2.6`` ``intel/2018a`` ``3.4.1`` ``foss/2018a`` ========= =============== .. _list_software_future_667: *future* ++++++++ python-future is the missing compatibility layer between Python 2 and Python 3. *homepage*: http://python-future.org/ ========== ================== ================================================ version versionsuffix toolchain ========== ================== ================================================ ``0.16.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``0.16.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``0.16.0`` ``-Python-3.6.3`` ``intel/2017b`` ``0.16.0`` ``-Python-3.6.6`` ``foss/2018b`` ========== ================== ================================================ .. _list_software_fxtract_764: *fxtract* +++++++++ Extract sequences from a fastx (fasta or fastq) file given a subsequence. *homepage*: https://github.com/ctSkennerton/fxtract ======= ================= version toolchain ======= ================= ``2.3`` ``GCCcore/8.2.0`` ======= ================= .. _list_software_letter_g: *G* --- :ref:`list_software_g2clib_563` - :ref:`list_software_g2lib_464` - :ref:`list_software_g2log_475` - :ref:`list_software_Gaia_370` - :ref:`list_software_GAMESS-US_661` - :ref:`list_software_gap_312` - :ref:`list_software_GapCloser_896` - :ref:`list_software_GapFiller_886` - :ref:`list_software_GARLI_367` - :ref:`list_software_GAT_220` - :ref:`list_software_GATE_289` - :ref:`list_software_GATK_295` - :ref:`list_software_Gblocks_709` - :ref:`list_software_gbs2ploidy_1023` - :ref:`list_software_gc_202` - :ref:`list_software_GC3Pie_475` - :ref:`list_software_GCC_205` - :ref:`list_software_GCCcore_630` - :ref:`list_software_gcccuda_714` - :ref:`list_software_GConf_461` - :ref:`list_software_Gctf_388` - :ref:`list_software_GD_139` - :ref:`list_software_GDAL_280` - :ref:`list_software_GDB_205` - :ref:`list_software_gdbgui_626` - :ref:`list_software_gdc-client_986` - :ref:`list_software_GDCHART_509` - :ref:`list_software_GDCM_283` - :ref:`list_software_GDGraph_637` - :ref:`list_software_gdist_539` - :ref:`list_software_Gdk-Pixbuf_945` - :ref:`list_software_Geant4_547` - :ref:`list_software_gearshifft_1059` - :ref:`list_software_GEM-library_1019` - :ref:`list_software_GEMMA_359` - :ref:`list_software_gencore_variant_detection_2645` - :ref:`list_software_GeneMark-ET_976` - :ref:`list_software_GenomeMapper_1216` - :ref:`list_software_GenomeTester4_1286` - :ref:`list_software_GenomeThreader_1418` - :ref:`list_software_GenotypeHarmonizer_1898` - :ref:`list_software_gensim_643` - :ref:`list_software_geopy_548` - :ref:`list_software_GEOS_302` - :ref:`list_software_Gerris_620` - :ref:`list_software_GETORB_451` - :ref:`list_software_gettext_773` - :ref:`list_software_GffCompare_986` - :ref:`list_software_gffread_719` - :ref:`list_software_gflags_628` - :ref:`list_software_GFOLD_364` - :ref:`list_software_GHC_210` - :ref:`list_software_Ghostscript_1178` - :ref:`list_software_giflib_621` - :ref:`list_software_gifsicle_838` - :ref:`list_software_GIMIC_361` - :ref:`list_software_gimkl_532` - :ref:`list_software_gimpi_534` - :ref:`list_software_gimpic_633` - :ref:`list_software_GIMPS_384` - :ref:`list_software_giolf_529` - :ref:`list_software_giolfc_628` - :ref:`list_software_git_324` - :ref:`list_software_git-lfs_694` - :ref:`list_software_GitPython_934` - :ref:`list_software_Givaro_616` - :ref:`list_software_Giza_395` - :ref:`list_software_GL2PS_360` - :ref:`list_software_Glade_477` - :ref:`list_software_glew_431` - :ref:`list_software_GLib_350` - :ref:`list_software_glibc_513` - :ref:`list_software_GLibmm_568` - :ref:`list_software_GLIMMER_525` - :ref:`list_software_GlimmerHMM_943` - :ref:`list_software_GLM_224` - :ref:`list_software_GlobalArrays_1219` - :ref:`list_software_Globus-CLI_881` - :ref:`list_software_GlobusConnectPersonal_2170` - :ref:`list_software_glog_425` - :ref:`list_software_GLPK_302` - :ref:`list_software_glproto_775` - :ref:`list_software_GMAP-GSNAP_715` - :ref:`list_software_GMP_228` - :ref:`list_software_gmpich_632` - :ref:`list_software_gmpolf_645` - :ref:`list_software_gmpy2_495` - :ref:`list_software_gmsh_431` - :ref:`list_software_GMT_232` - :ref:`list_software_gmvapich2_897` - :ref:`list_software_gmvolf_651` - :ref:`list_software_GNU_234` - :ref:`list_software_gnuplot_777` - :ref:`list_software_GnuTLS_541` - :ref:`list_software_Go_182` - :ref:`list_software_GObject-Introspection_2108` - :ref:`list_software_golf_424` - :ref:`list_software_gomkl_538` - :ref:`list_software_gompi_540` - :ref:`list_software_gompic_639` - :ref:`list_software_google-java-format_1794` - :ref:`list_software_googletest_1085` - :ref:`list_software_GP2C_268` - :ref:`list_software_GPAW_303` - :ref:`list_software_GPAW-setups_1024` - :ref:`list_software_gperf_532` - :ref:`list_software_gperftools_1093` - :ref:`list_software_gpustat_776` - :ref:`list_software_Grace_482` - :ref:`list_software_grace_514` - :ref:`list_software_Gradle_591` - :ref:`list_software_gradunwarp_1083` - :ref:`list_software_graph-tool_1021` - :ref:`list_software_Graphene_810` - :ref:`list_software_GraphicsMagick_1405` - :ref:`list_software_Graphviz_843` - :ref:`list_software_graphviz_875` - :ref:`list_software_GRASS_384` - :ref:`list_software_Greenlet_822` - :ref:`list_software_Grep_398` - :ref:`list_software_grib_api_829` - :ref:`list_software_GRIT_310` - :ref:`list_software_GRNBoost_750` - :ref:`list_software_GroIMP_526` - :ref:`list_software_GROMACS_524` - :ref:`list_software_GromacsWrapper_1453` - :ref:`list_software_GroopM_596` - :ref:`list_software_gsettings-desktop-schemas_2576` - :ref:`list_software_GSL_230` - :ref:`list_software_gSOAP_410` - :ref:`list_software_GST-plugins-base_1509` - :ref:`list_software_GStreamer_906` - :ref:`list_software_GTDB-Tk_525` - :ref:`list_software_gtest_551` - :ref:`list_software_GTK+_273` - :ref:`list_software_GtkSourceView_1330` - :ref:`list_software_GTOOL_389` - :ref:`list_software_GTS_238` - :ref:`list_software_guenomu_768` - :ref:`list_software_Guile_502` - :ref:`list_software_GULP_312` - :ref:`list_software_Gurobi_616` - :ref:`list_software_gzip_442` .. _list_software_g2clib_563: *g2clib* ++++++++ Library contains GRIB2 encoder/decoder ('C' version). *homepage*: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ ========= ===================================================================================================== version toolchain ========= ===================================================================================================== ``1.6.0`` ``GCCcore/8.3.0``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ========= ===================================================================================================== .. _list_software_g2lib_464: *g2lib* +++++++ Library contains GRIB2 encoder/decoder and search/indexing routines. *homepage*: http://www.nco.ncep.noaa.gov/pmb/codes/GRIB2/ ========= ================================================== version toolchain ========= ================================================== ``1.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.1.0`` ``GCCcore/8.3.0``, ``foss/2018b``, ``intel/2018b`` ========= ================================================== .. _list_software_g2log_475: *g2log* +++++++ g2log, efficient asynchronous logger using C++11 *homepage*: https://sites.google.com/site/kjellhedstrom2//g2log-efficient-background-io-processign-with-c11 ======= ============== version toolchain ======= ============== ``1.0`` ``foss/2016b`` ======= ============== .. _list_software_Gaia_370: *Gaia* ++++++ Gaia is a C++ library with python bindings which implements similarity measures and classifications on the results of audio analysis, and generates classification models that Essentia can use to compute high-level description of music. *homepage*: https://github.com/MTG/gaia ========= ================== ================= version versionsuffix toolchain ========= ================== ================= ``2.4.5`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ========= ================== ================= .. _list_software_GAMESS-US_661: *GAMESS-US* +++++++++++ The General Atomic and Molecular Electronic Structure System (GAMESS) is a general ab initio quantum chemistry package. *homepage*: http://www.msg.chem.iastate.edu/gamess/index.html =============== ============= =============== version versionsuffix toolchain =============== ============= =============== ``20141205-R1`` ``intel/2016a`` ``20170420-R1`` ``intel/2016b`` ``20170420-R1`` ``-sockets`` ``intel/2016b`` ``20180214-R1`` ``foss/2016b`` ``20180214-R1`` ``-sockets`` ``foss/2016b`` =============== ============= =============== .. _list_software_gap_312: *gap* +++++ GAP is a system for computational discrete algebra, with particular emphasis on Computational Group Theory. *homepage*: https://www.gap-system.org ========= =============== version toolchain ========= =============== ``4.9.3`` ``intel/2018b`` ========= =============== .. _list_software_GapCloser_896: *GapCloser* +++++++++++ GapCloser is designed to close the gaps emerging during the scaffolding process by SOAPdenovo or other assembler, using the abundant pair relationships of short reads. *homepage*: https://sourceforge.net/projects/soapdenovo2/files/GapCloser/ =========== =============================== version toolchain =========== =============================== ``1.12-r6`` ``foss/2018a``, ``intel/2017b`` =========== =============================== .. _list_software_GapFiller_886: *GapFiller* +++++++++++ GapFiller is a seed-and-extend local assembler to fill the gap within paired reads. It can be used for both DNA and RNA and it has been tested on Illumina data. *homepage*: https://sourceforge.net/projects/gapfiller ========= =============== version toolchain ========= =============== ``2.1.1`` ``intel/2017a`` ========= =============== .. _list_software_GARLI_367: *GARLI* +++++++ GARLI, Genetic Algorithm for Rapid Likelihood Inference is a program for inferring phylogenetic trees. Using an approach similar to a classical genetic algorithm, it rapidly searches the space of evolutionary trees and model parameters to find the solution maximizing the likelihood score. It implements nucleotide, amino acid and codon-based models of sequence evolution, and runs on all platforms. *homepage*: https://code.google.com/archive/p/garli/ ======== =============== version toolchain ======== =============== ``2.01`` ``gompi/2019a`` ======== =============== .. _list_software_GAT_220: *GAT* +++++ The Genomic Association Tester (GAT) is a tool for computing the significance of overlap between multiple sets of genomic intervals. GAT estimates significance based on simulation. *homepage*: https://gat.readthedocs.io/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.2.2`` ``-Python-2.7.11`` ``foss/2016a`` ========= ================== ============== .. _list_software_GATE_289: *GATE* ++++++ GATE is an advanced opensource software developed by the international OpenGATE collaboration and dedicated to the numerical simulations in medical imaging. It currently supports simulations of Emission Tomography (Positron Emission Tomography - PET and Single Photon Emission Computed Tomography - SPECT), and Computed Tomography *homepage*: http://www.opengatecollaboration.org/ =========== =============================== =============================== version versionsuffix toolchain =========== =============================== =============================== ``6.2`` ``-Python-2.7.11`` ``intel/2016a`` ``7.1`` ``-Python-2.7.11`` ``intel/2016a`` ``7.2`` ``-Python-2.7.11`` ``intel/2016a`` ``8.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``8.0`` ``-Python-2.7.14-Geant4-10.04`` ``intel/2017b`` ``8.1.p01`` ``-Python-2.7.15`` ``foss/2018b`` ``8.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``8.2`` ``-Python-2.7.15`` ``foss/2018b`` =========== =============================== =============================== .. _list_software_GATK_295: *GATK* ++++++ The Genome Analysis Toolkit or GATK is a software package developed at the Broad Institute to analyse next-generation resequencing data. The toolkit offers a wide variety of tools, with a primary focus on variant discovery and genotyping as well as strong emphasis on data quality assurance. Its robust architecture, powerful processing engine and high-performance computing features make it capable of taking on projects of any size. *homepage*: https://www.broadinstitute.org/gatk/ ============ =================== ================= version versionsuffix toolchain ============ =================== ================= ``1.0.5083`` ``system`` ``2.5-2`` ``-Java-1.7.0_10`` ``system`` ``2.6-5`` ``-Java-1.7.0_10`` ``system`` ``2.7-4`` ``system`` ``2.7-4`` ``-Java-1.7.0_10`` ``system`` ``2.8-1`` ``-Java-1.7.0_10`` ``system`` ``3.0-0`` ``-Java-1.7.0_10`` ``system`` ``3.3-0`` ``-Java-1.7.0_21`` ``system`` ``3.3-0`` ``-Java-1.7.0_80`` ``system`` ``3.3-0`` ``-Java-1.8.0_66`` ``system`` ``3.5`` ``-Java-1.8.0_66`` ``system`` ``3.5`` ``-Java-1.8.0_74`` ``system`` ``3.6`` ``-Java-1.8.0_92`` ``system`` ``3.7`` ``-Java-1.8.0_112`` ``system`` ``3.8-0`` ``-Java-1.8.0_144`` ``system`` ``4.0.1.2`` ``-Java-1.8`` ``system`` ``4.0.4.0`` ``-Python-2.7.14`` ``intel/2018a`` ``4.0.4.0`` ``-Python-3.6.4`` ``intel/2018a`` ``4.0.5.1`` ``-Python-3.6.4`` ``foss/2018a`` ``4.0.7.0`` ``-Python-2.7.14`` ``intel/2018a`` ``4.0.7.0`` ``-Python-3.6.4`` ``intel/2018a`` ``4.0.8.1`` ``-Python-2.7.15`` ``foss/2018b`` ``4.0.8.1`` ``-Python-3.6.6`` ``foss/2018b`` ``4.0.10.0`` ``-Python-3.6.6`` ``foss/2018b`` ``4.0.12.0`` ``-Python-3.6.6`` ``foss/2018b`` ``4.1.0.0`` ``-Python-3.6.6`` ``foss/2018b`` ``4.1.2.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` ``4.1.3.0`` ``-Java-1.8`` ``GCCcore/8.3.0`` ============ =================== ================= .. _list_software_Gblocks_709: *Gblocks* +++++++++ Selection of conserved blocks from multiple alignments for their use in phylogenetic analysis *homepage*: http://molevol.cmima.csic.es/castresana/Gblocks.html ========= ========== version toolchain ========= ========== ``0.91b`` ``system`` ========= ========== .. _list_software_gbs2ploidy_1023: *gbs2ploidy* ++++++++++++ Inference of Ploidy from (Genotyping-by-Sequencing) GBS Data *homepage*: https://cran.r-project.org/web/packages/gbs2ploidy ======= ============= =============== version versionsuffix toolchain ======= ============= =============== ``1.0`` ``-R-3.4.3`` ``intel/2017b`` ======= ============= =============== .. _list_software_gc_202: *gc* ++++ The Boehm-Demers-Weiser conservative garbage collector can be used as a garbage collecting replacement for C malloc or C++ new. *homepage*: http://hboehm.info/gc/ ========== ================================== version toolchain ========== ================================== ``7.4.4`` ``GCC/4.9.3-2.25``, ``foss/2016a`` ``7.6.0`` ``GCCcore/6.4.0`` ``7.6.4`` ``GCCcore/7.3.0`` ``7.6.10`` ``GCCcore/8.2.0`` ``7.6.12`` ``GCCcore/8.3.0`` ========== ================================== .. _list_software_GC3Pie_475: *GC3Pie* ++++++++ GC3Pie is a Python package for running large job campaigns on diverse batch-oriented execution environments. *homepage*: https://gc3pie.readthedocs.org ========= ========== version toolchain ========= ========== ``2.4.2`` ``system`` ``2.5.0`` ``system`` ``2.5.2`` ``system`` ========= ========== .. _list_software_GCC_205: *GCC* +++++ The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). *homepage*: http://gcc.gnu.org/ ========== =================== ========== version versionsuffix toolchain ========== =================== ========== ``4.8.1`` ``system`` ``4.8.1`` ``-CLooG`` ``system`` ``4.8.2`` ``system`` ``4.8.2`` ``-CLooG`` ``system`` ``4.8.2`` ``-CLooG-multilib`` ``system`` ``4.8.2`` ``-multilib`` ``system`` ``4.8.3`` ``system`` ``4.8.3`` ``-CLooG-multilib`` ``system`` ``4.8.4`` ``system`` ``4.8.4`` ``-CLooG`` ``system`` ``4.8.4`` ``-CLooG-multilib`` ``system`` ``4.8.5`` ``system`` ``4.9.0`` ``system`` ``4.9.0`` ``-CLooG`` ``system`` ``4.9.0`` ``-CLooG-multilib`` ``system`` ``4.9.1`` ``system`` ``4.9.1`` ``-CLooG`` ``system`` ``4.9.1`` ``-CLooG-multilib`` ``system`` ``4.9.2`` ``system`` ``4.9.2`` ``-CLooG`` ``system`` ``4.9.2`` ``-CLooG-multilib`` ``system`` ``4.9.2`` ``-binutils-2.25`` ``system`` ``4.9.3`` ``system`` ``4.9.3`` ``-2.25`` ``system`` ``4.9.3`` ``-binutils-2.25`` ``system`` ``4.9.4`` ``-2.25`` ``system`` ``5.1.0`` ``system`` ``5.1.0`` ``-binutils-2.25`` ``system`` ``5.2.0`` ``system`` ``5.3.0`` ``system`` ``5.3.0`` ``-2.26`` ``system`` ``5.4.0`` ``-2.26`` ``system`` ``5.5.0`` ``-2.26`` ``system`` ``6.1.0`` ``-2.27`` ``system`` ``6.2.0`` ``-2.27`` ``system`` ``6.3.0`` ``-2.27`` ``system`` ``6.3.0`` ``-2.28`` ``system`` ``6.4.0`` ``-2.28`` ``system`` ``7.1.0`` ``-2.28`` ``system`` ``7.2.0`` ``-2.29`` ``system`` ``7.3.0`` ``-2.30`` ``system`` ``7.4.0`` ``-2.31.1`` ``system`` ``8.1.0`` ``-2.30`` ``system`` ``8.2.0`` ``-2.31.1`` ``system`` ``8.3.0`` ``system`` ``8.3.0`` ``-2.32`` ``system`` ``9.1.0`` ``-2.32`` ``system`` ``9.2.0`` ``-2.32`` ``system`` ``system`` ``system`` ``system`` ``-2.29`` ``system`` ========== =================== ========== .. _list_software_GCCcore_630: *GCCcore* +++++++++ The GNU Compiler Collection includes front ends for C, C++, Objective-C, Fortran, Java, and Ada, as well as libraries for these languages (libstdc++, libgcj,...). *homepage*: http://gcc.gnu.org/ ========== ========== version toolchain ========== ========== ``4.9.2`` ``system`` ``4.9.3`` ``system`` ``4.9.4`` ``system`` ``5.3.0`` ``system`` ``5.4.0`` ``system`` ``5.5.0`` ``system`` ``6.1.0`` ``system`` ``6.2.0`` ``system`` ``6.3.0`` ``system`` ``6.4.0`` ``system`` ``6.5.0`` ``system`` ``7.1.0`` ``system`` ``7.2.0`` ``system`` ``7.3.0`` ``system`` ``7.4.0`` ``system`` ``8.1.0`` ``system`` ``8.2.0`` ``system`` ``8.3.0`` ``system`` ``9.1.0`` ``system`` ``9.2.0`` ``system`` ``system`` ``system`` ========== ========== .. _list_software_gcccuda_714: *gcccuda* +++++++++ GNU Compiler Collection (GCC) based compiler toolchain, along with CUDA toolkit. *homepage*: (none) =========== ========== version toolchain =========== ========== ``2016.08`` ``system`` ``2017b`` ``system`` ``2018a`` ``system`` ``2018b`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` =========== ========== .. _list_software_GConf_461: *GConf* +++++++ GConf is a system for storing application preferences. It is intended for user preferences; not configuration of something like Apache, or arbitrary data storage. *homepage*: https://projects.gnome.org/gconf/ ========= ===================================================================================================================== version toolchain ========= ===================================================================================================================== ``3.2.6`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ========= ===================================================================================================================== .. _list_software_Gctf_388: *Gctf* ++++++ Gctf: real-time CTF determination and correction, Kai Zhang, 2016 *homepage*: https://www.mrc-lmb.cam.ac.uk/kzhang/ ======== ========== version toolchain ======== ========== ``1.06`` ``system`` ======== ========== .. _list_software_GD_139: *GD* ++++ GD.pm - Interface to Gd Graphics Library *homepage*: https://github.com/lstein/Perl-GD ======== ================ ================= version versionsuffix toolchain ======== ================ ================= ``2.66`` ``-Perl-5.24.0`` ``foss/2016b`` ``2.68`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` ``2.69`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` ======== ================ ================= .. _list_software_GDAL_280: *GDAL* ++++++ GDAL is a translator library for raster geospatial data formats that is released under an X/MIT style Open Source license by the Open Source Geospatial Foundation. As a library, it presents a single abstract data model to the calling application for all supported formats. It also comes with a variety of useful commandline utilities for data translation and processing. *homepage*: https://www.gdal.org ========= ============================== ================================================================ version versionsuffix toolchain ========= ============================== ================================================================ ``2.0.2`` ``foss/2016a``, ``intel/2016a`` ``2.1.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``2.1.1`` ``foss/2016a`` ``2.1.1`` ``-Python-2.7.12`` ``intel/2016b`` ``2.1.2`` ``-Python-2.7.12`` ``intel/2016b`` ``2.1.3`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``2.1.3`` ``-Python-2.7.13`` ``intel/2017a`` ``2.1.3`` ``-Python-3.6.1`` ``intel/2017a`` ``2.2.0`` ``-Python-2.7.13-HDF5-1.8.18`` ``intel/2017a`` ``2.2.0`` ``-Python-2.7.13-HDF5-HDF`` ``intel/2017a`` ``2.2.0`` ``-Python-3.6.1`` ``intel/2017a`` ``2.2.2`` ``-Python-2.7.14`` ``intel/2017b`` ``2.2.2`` ``-Python-2.7.14-HDF5-1.8.19`` ``intel/2017b`` ``2.2.3`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``2.2.3`` ``-Python-2.7.15`` ``foss/2018b`` ``2.2.3`` ``-Python-3.6.3`` ``foss/2017b`` ``2.2.3`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` ``2.2.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.0.0`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ``3.0.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``3.0.2`` ``-Python-3.7.4`` ``intel/2019b`` ========= ============================== ================================================================ .. _list_software_GDB_205: *GDB* +++++ The GNU Project Debugger *homepage*: http://www.gnu.org/software/gdb/gdb.html ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``7.8.2`` ``GCC/4.9.2`` ``7.9`` ``GCC/4.9.2`` ``7.10.1`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``7.11`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``7.11.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``8.0.1`` ``-Python-2.7.14`` ``foss/2017b`` ``8.0.1`` ``-Python-3.6.3`` ``foss/2017b`` ``8.1`` ``-Python-2.7.14`` ``foss/2018a`` ``8.1.1`` ``-Python-2.7.14`` ``intel/2018a`` ``8.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================== =============================== .. _list_software_gdbgui_626: *gdbgui* ++++++++ Browser-based frontend to gdb (gnu debugger). Add breakpoints, view the stack, visualize data structures, and more in C, C++, Go, Rust, and Fortran. Run gdbgui from the terminal and a new tab will open in your browser. *homepage*: https://gdbgui.com ============ ================= ================= version versionsuffix toolchain ============ ================= ================= ``0.13.1.2`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ============ ================= ================= .. _list_software_gdc-client_986: *gdc-client* ++++++++++++ The gdc-client provides several convenience functions over the GDC API which provides general download/upload via HTTPS. *homepage*: https://gdc.nci.nih.gov/access-data/gdc-data-transfer-tool ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``1.0.1`` ``-Python-2.7.12`` ``intel/2016b`` ``1.3.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` ``1.3.0`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== =============================== .. _list_software_GDCHART_509: *GDCHART* +++++++++ Easy to use C API, high performance library to create charts and graphs in PNG, GIF and WBMP format. *homepage*: http://users.fred.net/brv/chart ============= ================= version toolchain ============= ================= ``0.11.5dev`` ``GCCcore/8.2.0`` ============= ================= .. _list_software_GDCM_283: *GDCM* ++++++ Grassroots DICOM: Cross-platform DICOM implementation *homepage*: https://sourceforge.net/projects/gdcm ========= ================= version toolchain ========= ================= ``2.8.8`` ``GCCcore/6.4.0`` ``2.8.9`` ``GCCcore/7.3.0`` ``3.0.4`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_GDGraph_637: *GDGraph* +++++++++ GDGraph is a Perl package to generate charts *homepage*: https://metacpan.org/release/GDGraph ======== ================ =============== version versionsuffix toolchain ======== ================ =============== ``1.54`` ``-Perl-5.26.1`` ``intel/2018a`` ``1.54`` ``-Perl-5.28.0`` ``foss/2018b`` ======== ================ =============== .. _list_software_gdist_539: *gdist* +++++++ The gdist module is a Cython interface to a C++ library (http://code.google.com/p/geodesic/) for computing geodesic distance which is the length of shortest line between two vertices on a triangulated mesh in three dimensions, such that the line lies on the surface. *homepage*: https://pypi.python.org/pypi/gdist ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.0.3`` ``-Python-2.7.11`` ``intel/2016a`` ========= ================== =============== .. _list_software_Gdk-Pixbuf_945: *Gdk-Pixbuf* ++++++++++++ The Gdk Pixbuf is a toolkit for image loading and pixel buffer manipulation. It is used by GTK+ 2 and GTK+ 3 to load and manipulate images. In the past it was distributed as part of GTK+ 2 but it was split off into a separate package in preparation for the change to GTK+ 3. *homepage*: https://developer.gnome.org/gdk-pixbuf/stable/ =========== ==================================================================================== version toolchain =========== ==================================================================================== ``2.32.3`` ``intel/2016a`` ``2.35.1`` ``foss/2016a``, ``intel/2016a`` ``2.36.0`` ``foss/2016b``, ``intel/2016b`` ``2.36.8`` ``intel/2017a`` ``2.36.10`` ``intel/2017a`` ``2.36.11`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2018b``, ``intel/2017b``, ``intel/2018a`` ``2.36.12`` ``foss/2018b``, ``fosscuda/2018b`` ``2.38.1`` ``GCCcore/8.2.0`` =========== ==================================================================================== .. _list_software_Geant4_547: *Geant4* ++++++++ Geant4 is a toolkit for the simulation of the passage of particles through matter. Its areas of application include high energy, nuclear and accelerator physics, as well as studies in medical and space science. *homepage*: http://geant4.cern.ch/ ============= ================================================================ version toolchain ============= ================================================================ ``9.5.p02`` ``intel/2016a`` ``9.6.p04`` ``intel/2016a`` ``10.01.p03`` ``intel/2016a`` ``10.02.p01`` ``intel/2016a`` ``10.03.p03`` ``foss/2017b``, ``intel/2017b`` ``10.04`` ``intel/2017b`` ``10.5`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018b`` ============= ================================================================ .. _list_software_gearshifft_1059: *gearshifft* ++++++++++++ Benchmark Suite for Heterogenuous FFT Implementations *homepage*: https://github.com/mpicbg-scicomp/gearshifft ========= ============== version toolchain ========= ============== ``0.4.0`` ``foss/2019a`` ========= ============== .. _list_software_GEM-library_1019: *GEM-library* +++++++++++++ Next-generation sequencing platforms (Illumina/Solexa, ABI/SOLiD, etc.) call for powerful and very optimized tools to index/analyze huge genomes. The GEM library strives to be a true "next-generation" tool for handling any kind of sequence data, offering state-of-the-art algorithms and data structures specifically tailored to this demanding task. At the moment, efficient indexing and searching algorithms based on the Burrows-Wheeler transform (BWT) have been implemented. The library core is written in C for maximum speed, with concise interfaces to higher-level programming languages like OCaml and Python. Many high-performance standalone programs (mapper, splice mapper, etc.) are provided along with the library; in general, new algorithms and tools can be easily implemented on the top of it. *homepage*: http://algorithms.cnag.cat/wiki/The_GEM_library =================== =============================== ========== version versionsuffix toolchain =================== =============================== ========== ``20130406-045632`` ``_pre-release-3_Linux-x86_64`` ``system`` =================== =============================== ========== .. _list_software_GEMMA_359: *GEMMA* +++++++ Genome-wide Efficient Mixed Model Association *homepage*: https://github.com/genetics-statistics/GEMMA ========== ============================== version toolchain ========== ============================== ``0.97`` ``foss/2016b``, ``foss/2017a`` ``0.98.1`` ``foss/2018b`` ========== ============================== .. _list_software_gencore_variant_detection_2645: *gencore_variant_detection* +++++++++++++++++++++++++++ This is a bundled install of many software packages for doing variant detection analysis. *homepage*: https://nyuad-cgsb.github.io/variant_detection/public/index.html ======= ========== version toolchain ======= ========== ``1.0`` ``system`` ======= ========== .. _list_software_GeneMark-ET_976: *GeneMark-ET* +++++++++++++ Eukaryotic gene prediction suite with automatic training *homepage*: http://exon.gatech.edu/GeneMark ======== ================= version toolchain ======== ================= ``4.38`` ``GCCcore/8.2.0`` ======== ================= .. _list_software_GenomeMapper_1216: *GenomeMapper* ++++++++++++++ GenomeMapper is a short read mapping tool designed for accurate read alignments. It quickly aligns millions of reads either with ungapped or gapped alignments. This version is used to align against a single reference. If you are unsure which one is the appropriate GenomeMapper, you might want to use this one. *homepage*: https://1001genomes.org/software/genomemapper_singleref.html ========= ============== version toolchain ========= ============== ``0.4.4`` ``foss/2016a`` ========= ============== .. _list_software_GenomeTester4_1286: *GenomeTester4* +++++++++++++++ A toolkit for performing set operations - union, intersection and complement - on k-mer lists. *homepage*: https://github.com/bioinfo-ut/GenomeTester4 ======= =============== version toolchain ======= =============== ``4.0`` ``intel/2018a`` ======= =============== .. _list_software_GenomeThreader_1418: *GenomeThreader* ++++++++++++++++ GenomeThreader is a software tool to compute gene structure predictions. *homepage*: http://genomethreader.org ========= ======================= ========== version versionsuffix toolchain ========= ======================= ========== ``1.7.1`` ``-Linux_x86_64-64bit`` ``system`` ========= ======================= ========== .. _list_software_GenotypeHarmonizer_1898: *GenotypeHarmonizer* ++++++++++++++++++++ The Genotype Harmonizer is an easy to use command-line tool that allows harmonization of genotype data stored using different file formats with different and potentially unknown strands. *homepage*: https://github.com/molgenis/systemsgenetics/wiki/Genotype-Harmonizer ========== ================== ========== version versionsuffix toolchain ========== ================== ========== ``1.4.14`` ``-Java-1.7.0_80`` ``system`` ========== ================== ========== .. _list_software_gensim_643: *gensim* ++++++++ Gensim is a Python library for topic modelling, document indexing and similarity retrieval with large corpora. *homepage*: https://pypi.python.org/pypi/gensim ========== ================== ============== version versionsuffix toolchain ========== ================== ============== ``0.13.2`` ``-Python-2.7.11`` ``foss/2016a`` ========== ================== ============== .. _list_software_geopy_548: *geopy* +++++++ geopy is a Python 2 and 3 client for several popular geocoding web services. *homepage*: https://github.com/geopy/geopy ========== ================= =============== version versionsuffix toolchain ========== ================= =============== ``1.11.0`` ``-Python-3.6.1`` ``intel/2017a`` ========== ================= =============== .. _list_software_GEOS_302: *GEOS* ++++++ GEOS (Geometry Engine - Open Source) is a C++ port of the Java Topology Suite (JTS) *homepage*: https://trac.osgeo.org/geos ========= ================== ================================================================ version versionsuffix toolchain ========= ================== ================================================================ ``3.5.0`` ``-Python-2.7.11`` ``intel/2016a`` ``3.5.0`` ``-Python-2.7.12`` ``intel/2016b`` ``3.6.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``3.6.1`` ``-Python-2.7.13`` ``intel/2017a`` ``3.6.1`` ``-Python-3.6.1`` ``intel/2017a`` ``3.6.2`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``3.6.2`` ``-Python-2.7.15`` ``foss/2018b`` ``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` ``3.6.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.01`` ``3.6.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` ``3.6.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.7.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ``3.7.2`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``3.8.0`` ``-Python-3.7.4`` ``iccifort/2019.5.281`` ========= ================== ================================================================ .. _list_software_Gerris_620: *Gerris* ++++++++ Gerris is a Free Software program for the solution of the partial differential equations describing fluid flow *homepage*: http://gfs.sourceforge.net/wiki/index.php/Main_Page ============ ============== version toolchain ============ ============== ``20131206`` ``foss/2017b`` ============ ============== .. _list_software_GETORB_451: *GETORB* ++++++++ GETORB software package contains programs to handle the orbital data records (ODRs) *homepage*: http://www.deos.tudelft.nl/ers/precorbs/tools/getorb_pack.shtml ========= =============== version toolchain ========= =============== ``2.3.2`` ``intel/2017a`` ========= =============== .. _list_software_gettext_773: *gettext* +++++++++ GNU 'gettext' is an important step for the GNU Translation Project, as it is an asset on which we may build many other steps. This package offers to programmers, translators, and even users, a well integrated set of tools and documentation *homepage*: https://www.gnu.org/software/gettext/ ============ ================== =================================================================================================== version versionsuffix toolchain ============ ================== =================================================================================================== ``0.18.2`` ``system`` ``0.19.4`` ``GCC/4.9.2``, ``system`` ``0.19.6`` ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``system`` ``0.19.7`` ``foss/2016a``, ``intel/2016a``, ``system`` ``0.19.8`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016.04``, ``foss/2016b``, ``intel/2016b``, ``system`` ``0.19.8.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` ``0.19.8.1`` ``-libxml2-2.9.7`` ``GCCcore/6.4.0`` ``0.20.1`` ``GCCcore/8.3.0``, ``system`` ============ ================== =================================================================================================== .. _list_software_GffCompare_986: *GffCompare* ++++++++++++ GffCompare provides classification and reference annotation mapping and matching statistics for RNA-Seq assemblies (transfrags) or other generic GFF/GTF files. *homepage*: https://github.com/gpertea/gffcompare ========== ================= version toolchain ========== ================= ``0.10.1`` ``foss/2016b`` ``0.10.6`` ``GCCcore/7.3.0`` ========== ================= .. _list_software_gffread_719: *gffread* +++++++++ GFF/GTF parsing utility providing format conversions, region filtering, FASTA sequence extraction and more. *homepage*: https://github.com/gpertea/gffread ========== ================= version toolchain ========== ================= ``0.9.12`` ``foss/2016b`` ``0.10.6`` ``GCCcore/7.3.0`` ``0.11.6`` ``GCCcore/8.3.0`` ========== ================= .. _list_software_gflags_628: *gflags* ++++++++ The gflags package contains a C++ library that implements commandline flags processing. It includes built-in support for standard types such as string and the ability to define flags in the source file in which they are used. *homepage*: https://github.com/gflags/gflags ========= =================================================== version toolchain ========= =================================================== ``2.1.2`` ``foss/2016a`` ``2.2.1`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` ``2.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= =================================================== .. _list_software_GFOLD_364: *GFOLD* +++++++ Generalized fold change for ranking differentially expressed genes from RNA-seq data *homepage*: http://www.tongji.edu.cn/~zhanglab/GFOLD/index.html ========= =============== version toolchain ========= =============== ``1.1.4`` ``intel/2016a`` ========= =============== .. _list_software_GHC_210: *GHC* +++++ The Glorious/Glasgow Haskell Compiler *homepage*: http://haskell.org/ghc/ ========== ========== version toolchain ========== ========== ``6.12.3`` ``system`` ========== ========== .. _list_software_Ghostscript_1178: *Ghostscript* +++++++++++++ Ghostscript is a versatile processor for PostScript data with the ability to render PostScript to different targets. It used to be part of the cups printing stack, but is no longer used for that. *homepage*: https://ghostscript.com ======== ================== ================================================== version versionsuffix toolchain ======== ================== ================================================== ``9.19`` ``intel/2016a``, ``intel/2016b`` ``9.20`` ``foss/2016b``, ``intel/2016b`` ``9.21`` ``intel/2017a`` ``9.22`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b`` ``9.22`` ``-cairo-1.14.12`` ``GCCcore/6.4.0`` ``9.23`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``9.23`` ``-cairo-1.14.12`` ``GCCcore/6.4.0`` ``9.27`` ``GCCcore/8.2.0`` ``9.50`` ``GCCcore/8.3.0`` ======== ================== ================================================== .. _list_software_giflib_621: *giflib* ++++++++ giflib is a library for reading and writing gif images. It is API and ABI compatible with libungif which was in wide use while the LZW compression algorithm was patented. *homepage*: http://libungif.sourceforge.net/ ========= ==================================== version toolchain ========= ==================================== ``5.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ========= ==================================== .. _list_software_gifsicle_838: *gifsicle* ++++++++++ Gifsicle is a command-line tool for creating, editing, and getting information about GIF images and animations. Making a GIF animation with gifsicle is easy. *homepage*: https://github.com/kohler/gifsicle ======== ================= version toolchain ======== ================= ``1.92`` ``GCCcore/8.2.0`` ======== ================= .. _list_software_GIMIC_361: *GIMIC* +++++++ The GIMIC program calculates magnetically induced currents in molecules. You need to provide this program with a density matrix in atomic-orbital (AO) basis and three (effective) magnetically perturbed AO density matrices in the proper format. Currently ACES2, Turbomole, G09, QChem, FERMION++, and LSDalton can produce these matrices. *homepage*: http://gimic.readthedocs.io ============== ================== =============== version versionsuffix toolchain ============== ================== =============== ``2018.04.20`` ``-Python-2.7.14`` ``intel/2018a`` ============== ================== =============== .. _list_software_gimkl_532: *gimkl* +++++++ GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI and MKL *homepage*: (none) ========== ========== version toolchain ========== ========== ``2.11.5`` ``system`` ``2017a`` ``system`` ``2018b`` ``system`` ========== ========== .. _list_software_gimpi_534: *gimpi* +++++++ GNU Compiler Collection (GCC) based compiler toolchain with Intel MPI. *homepage*: (none) ========== ========== version toolchain ========== ========== ``2.11.5`` ``system`` ``2017a`` ``system`` ``2017b`` ``system`` ``2018a`` ``system`` ``2018b`` ``system`` ========== ========== .. _list_software_gimpic_633: *gimpic* ++++++++ GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including IntelMPI for MPI support with CUDA features enabled. *homepage*: (none) ========= ========== version toolchain ========= ========== ``2017b`` ``system`` ========= ========== .. _list_software_GIMPS_384: *GIMPS* +++++++ GIMPS: Great Internet Mersenne Prime Search; it can be useful for limited stress testing of nodes, in user space *homepage*: http://www.mersenne.org/ =================== ============= version toolchain =================== ============= ``p95v279`` ``GCC/4.8.2`` ``p95v279.linux64`` ``system`` =================== ============= .. _list_software_giolf_529: *giolf* +++++++ GNU Compiler Collection (GCC) based compiler toolchain, including IntelMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. *homepage*: (none) ========= ========== version toolchain ========= ========== ``2017b`` ``system`` ``2018a`` ``system`` ========= ========== .. _list_software_giolfc_628: *giolfc* ++++++++ GCC based compiler toolchain __with CUDA support__, and including IntelMPI for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. *homepage*: (none) ========= ========== version toolchain ========= ========== ``2017b`` ``system`` ========= ========== .. _list_software_git_324: *git* +++++ Git is a free and open source distributed version control system designed to handle everything from small to very large projects with speed and efficiency. *homepage*: http://git-scm.com/ =========== ============= ================= version versionsuffix toolchain =========== ============= ================= ``1.8.5.6`` ``GCC/4.9.2`` ``2.2.2`` ``GCC/4.9.2`` ``2.4.1`` ``GCC/4.9.2`` ``2.8.0`` ``foss/2016a`` ``2.12.2`` ``foss/2016b`` ``2.13.1`` ``foss/2016b`` ``2.14.1`` ``GCCcore/6.4.0`` ``2.16.1`` ``foss/2018a`` ``2.18.0`` ``GCCcore/7.3.0`` ``2.19.1`` ``GCCcore/7.3.0`` ``2.21.0`` ``GCCcore/8.2.0`` ``2.21.0`` ``-nodocs`` ``GCCcore/8.2.0`` ``2.23.0`` ``GCCcore/8.3.0`` ``2.23.0`` ``-nodocs`` ``GCCcore/8.3.0`` =========== ============= ================= .. _list_software_git-lfs_694: *git-lfs* +++++++++ Git Large File Storage (LFS) replaces large files such as audio samples, videos, datasets, and graphics with text pointers inside Git, while storing the file contents on a remote server like GitHub.com *homepage*: https://git-lfs.github.com ========= ========== version toolchain ========= ========== ``1.1.1`` ``system`` ``2.7.1`` ``system`` ========= ========== .. _list_software_GitPython_934: *GitPython* +++++++++++ GitPython is a python library used to interact with Git repositories *homepage*: https://github.com/gitpython-developers/GitPython ========== ================= =============================== version versionsuffix toolchain ========== ================= =============================== ``2.1.11`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.0.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================= =============================== .. _list_software_Givaro_616: *Givaro* ++++++++ C++ library for arithmetic and algebraic computations *homepage*: http://givaro.forge.imag.fr/ ========= ============== version toolchain ========= ============== ``4.0.1`` ``foss/2016a`` ========= ============== .. _list_software_Giza_395: *Giza* ++++++ Giza is an open, lightweight scientific plotting library built on top of cairo that provides uniform output to multiple devices. *homepage*: https://danieljprice.github.io/giza/ ========= ============== version toolchain ========= ============== ``1.1.0`` ``foss/2018b`` ========= ============== .. _list_software_GL2PS_360: *GL2PS* +++++++ GL2PS: an OpenGL to PostScript printing library *homepage*: http://www.geuz.org/gl2ps/ ========= ================ ================================================================================================= version versionsuffix toolchain ========= ================ ================================================================================================= ``1.3.9`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.3.9`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` ``1.4.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ========= ================ ================================================================================================= .. _list_software_Glade_477: *Glade* +++++++ Glade is a RAD tool to enable quick & easy development of user interfaces for the GTK+ toolkit and the GNOME desktop environment. *homepage*: https://glade.gnome.org/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``3.8.5`` ``-Python-2.7.11`` ``intel/2016a`` ``3.8.5`` ``-Python-2.7.14`` ``intel/2017b`` ``3.8.6`` ``-Python-2.7.14`` ``intel/2018a`` ``3.8.6`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== =============== .. _list_software_glew_431: *glew* ++++++ The OpenGL Extension Wrangler Library The OpenGL Extension Wrangler Library (GLEW) is a cross-platform open-source C/C++ extension loading library. GLEW provides efficient run-time mechanisms for determining which OpenGL extensions are supported on the target platform. OpenGL core and extension functionality is exposed in a single header file. GLEW has been tested on a variety of operating systems, including Windows, Linux, Mac OS X, FreeBSD, Irix, and Solaris. *homepage*: http://glew.sourceforge.net/ ========= ================================= version toolchain ========= ================================= ``2.1.0`` ``GCCcore/8.2.0``, ``foss/2018b`` ========= ================================= .. _list_software_GLib_350: *GLib* ++++++ GLib is one of the base libraries of the GTK+ project *homepage*: https://www.gtk.org/ ========== ================================================= version toolchain ========== ================================================= ``2.42.1`` ``GCC/4.9.2`` ``2.44.0`` ``GCC/4.9.2`` ``2.47.5`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``2.48.0`` ``foss/2016a``, ``intel/2016a`` ``2.49.5`` ``foss/2016b``, ``intel/2016b`` ``2.52.0`` ``foss/2017a``, ``intel/2017a`` ``2.53.5`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``2.54.2`` ``GCCcore/6.4.0`` ``2.54.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.60.1`` ``GCCcore/8.2.0`` ``2.62.0`` ``GCCcore/8.3.0`` ========== ================================================= .. _list_software_glibc_513: *glibc* +++++++ The GNU C Library project provides the core libraries for the GNU system and GNU/Linux systems, as well as many other systems that use Linux as the kernel. *homepage*: https://www.gnu.org/software/libc/ ======== ================= version toolchain ======== ================= ``2.17`` ``GCCcore/6.4.0`` ``2.26`` ``GCCcore/6.4.0`` ``2.30`` ``GCCcore/8.3.0`` ======== ================= .. _list_software_GLibmm_568: *GLibmm* ++++++++ C++ bindings for Glib *homepage*: https://www.gtk.org/ ========== ======================================================= version toolchain ========== ======================================================= ``2.49.7`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========== ======================================================= .. _list_software_GLIMMER_525: *GLIMMER* +++++++++ Glimmer is a system for finding genes in microbial DNA, especially the genomes of bacteria, archaea, and viruses. *homepage*: http://www.cbcb.umd.edu/software/glimmer/ ========= ============================== version toolchain ========= ============================== ``3.02b`` ``foss/2016b``, ``foss/2018b`` ========= ============================== .. _list_software_GlimmerHMM_943: *GlimmerHMM* ++++++++++++ GlimmerHMM is a new gene finder based on a Generalized Hidden Markov Model. Although the gene finder conforms to the overall mathematical framework of a GHMM, additionally it incorporates splice site models adapted from the GeneSplicer program and a decision tree adapted from GlimmerM. It also utilizes Interpolated Markov Models for the coding and noncoding models. *homepage*: https://ccb.jhu.edu/software/glimmerhmm ========= ============================== version toolchain ========= ============================== ``3.0.4`` ``foss/2016b``, ``foss/2018b`` ========= ============================== .. _list_software_GLM_224: *GLM* +++++ OpenGL Mathematics (GLM) is a header only C++ mathematics library for graphics software based on the OpenGL Shading Language (GLSL) specifications. *homepage*: https://github.com/g-truc/glm =========== ================= version toolchain =========== ================= ``0.9.7.6`` ``intel/2016a`` ``0.9.8.3`` ``GCCcore/5.4.0`` ``0.9.9.0`` ``GCCcore/6.4.0`` =========== ================= .. _list_software_GlobalArrays_1219: *GlobalArrays* ++++++++++++++ Global Arrays (GA) is a Partitioned Global Address Space (PGAS) programming model *homepage*: https://hpc.pnl.gov/globalarrays ======= ============= =============== version versionsuffix toolchain ======= ============= =============== ``5.7`` ``intel/2018b`` ``5.7`` ``-peigs`` ``intel/2019a`` ======= ============= =============== .. _list_software_Globus-CLI_881: *Globus-CLI* ++++++++++++ A Command Line Wrapper over the Globus SDK for Python, which provides an interface to Globus services from the shell, and is suited to both interactive and simple scripting use cases. *homepage*: https://docs.globus.org/cli/ ========== ================= version toolchain ========== ================= ``1.11.0`` ``GCCcore/8.3.0`` ========== ================= .. _list_software_GlobusConnectPersonal_2170: *GlobusConnectPersonal* +++++++++++++++++++++++ Globus Connect Personal turns your laptop or other personal computer into a Globus endpoint with a just a few clicks. With Globus Connect Personal you can share and transfer files to/from a local machine—campus server, desktop computer or laptop—even if it's behind a firewall and you don't have administrator privileges. *homepage*: https://www.globus.org/globus-connect-personal ========= ========== version toolchain ========= ========== ``2.3.6`` ``system`` ========= ========== .. _list_software_glog_425: *glog* ++++++ A C++ implementation of the Google logging module. *homepage*: https://github.com/google/glog ========= =================================================== version toolchain ========= =================================================== ``0.3.4`` ``foss/2016a`` ``0.3.5`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` ``0.4.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= =================================================== .. _list_software_GLPK_302: *GLPK* ++++++ The GLPK (GNU Linear Programming Kit) package is intended for solving large-scale linear programming (LP), mixed integer programming (MIP), and other related problems. It is a set of routines written in ANSI C and organized in the form of a callable library. *homepage*: https://www.gnu.org/software/glpk/ ======== ======================================================= version toolchain ======== ======================================================= ``4.58`` ``foss/2016a``, ``intel/2016a`` ``4.60`` ``GCCcore/5.4.0``, ``intel/2016b`` ``4.61`` ``intel/2017a`` ``4.65`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ======== ======================================================= .. _list_software_glproto_775: *glproto* +++++++++ X protocol and ancillary headers *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========== ================================================= version toolchain ========== ================================================= ``1.4.17`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========== ================================================= .. _list_software_GMAP-GSNAP_715: *GMAP-GSNAP* ++++++++++++ GMAP: A Genomic Mapping and Alignment Program for mRNA and EST Sequences GSNAP: Genomic Short-read Nucleotide Alignment Program *homepage*: http://research-pub.gene.com/gmap/ ============== =============== version toolchain ============== =============== ``2016-05-01`` ``foss/2016a`` ``2016-11-07`` ``foss/2016b`` ``2018-05-11`` ``intel/2018a`` ``2018-07-04`` ``intel/2018a`` ``2019-03-15`` ``foss/2018b`` ============== =============== .. _list_software_GMP_228: *GMP* +++++ GMP is a free library for arbitrary precision arithmetic, operating on signed integers, rational numbers, and floating point numbers. *homepage*: http://gmplib.org/ ========== ===================================================================================================================================================== version toolchain ========== ===================================================================================================================================================== ``4.3.2`` ``system`` ``5.1.3`` ``GCC/4.8.2`` ``6.0.0`` ``GCC/4.9.2`` ``6.0.0a`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` ``6.1.0`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``6.1.1`` ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``6.1.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b`` ========== ===================================================================================================================================================== .. _list_software_gmpich_632: *gmpich* ++++++++ gcc and GFortran based compiler toolchain, including MPICH for MPI support. *homepage*: (none) =========== ========== version toolchain =========== ========== ``2016a`` ``system`` ``2017.08`` ``system`` =========== ========== .. _list_software_gmpolf_645: *gmpolf* ++++++++ gcc and GFortran based compiler toolchain, MPICH for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. *homepage*: (none) =========== ========== version toolchain =========== ========== ``2016a`` ``system`` ``2017.10`` ``system`` =========== ========== .. _list_software_gmpy2_495: *gmpy2* +++++++ GMP/MPIR, MPFR, and MPC interface to Python 2.6+ and 3.x *homepage*: https://github.com/aleaxit/gmpy =========== ================== =============================== version versionsuffix toolchain =========== ================== =============================== ``2.0.8`` ``-Python-2.7.13`` ``intel/2017a`` ``2.0.8`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2.0.8`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``2.1.0b1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2.1.0b1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` =========== ================== =============================== .. _list_software_gmsh_431: *gmsh* ++++++ Gmsh is a 3D finite element grid generator with a build-in CAD engine and post-processor. *homepage*: http://geuz.org/gmsh ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``3.0.6`` ``-Python-2.7.14`` ``foss/2017b`` ``3.0.6`` ``-Python-3.6.6`` ``foss/2018b`` ``4.2.2`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================== ============== .. _list_software_GMT_232: *GMT* +++++ GMT is an open source collection of about 80 command-line tools for manipulating geographic and Cartesian data sets (including filtering, trend fitting, gridding, projecting, etc.) and producing PostScript illustrations ranging from simple x-y plots via contour maps to artificially illuminated surfaces and 3D perspective views; the GMT supplements add another 40 more specialized and discipline-specific tools. *homepage*: https://gmt.soest.hawaii.edu/ ========== =============================== version toolchain ========== =============================== ``4.5.17`` ``foss/2018a`` ``5.4.1`` ``intel/2017a`` ``5.4.3`` ``foss/2018a``, ``intel/2017b`` ``5.4.5`` ``foss/2019a`` ========== =============================== .. _list_software_gmvapich2_897: *gmvapich2* +++++++++++ GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support. *homepage*: (none) ========== ========== version toolchain ========== ========== ``1.7.20`` ``system`` ``2016a`` ``system`` ========== ========== .. _list_software_gmvolf_651: *gmvolf* ++++++++ GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support, OpenBLAS (BLAS and LAPACK support), FFTW and ScaLAPACK. *homepage*: (none) ========== ========== version toolchain ========== ========== ``1.7.20`` ``system`` ``2016a`` ``system`` ========== ========== .. _list_software_GNU_234: *GNU* +++++ Compiler-only toolchain with GCC and binutils. *homepage*: http://www.gnu.org/software/ ============== ========== version toolchain ============== ========== ``4.9.2-2.25`` ``system`` ``4.9.3-2.25`` ``system`` ``5.1.0-2.25`` ``system`` ============== ========== .. _list_software_gnuplot_777: *gnuplot* +++++++++ Portable interactive, function plotting utility *homepage*: http://gnuplot.sourceforge.net/ ========= ================================================================ version toolchain ========= ================================================================ ``5.0.3`` ``foss/2016a``, ``intel/2016a`` ``5.0.5`` ``foss/2016b``, ``intel/2016b`` ``5.0.6`` ``intel/2017a`` ``5.2.2`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``5.2.5`` ``foss/2018b`` ``5.2.6`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b`` ========= ================================================================ .. _list_software_GnuTLS_541: *GnuTLS* ++++++++ GnuTLS is a secure communications library implementing the SSL, TLS and DTLS protocols and technologies around them. It provides a simple C language application programming interface (API) to access the secure communications protocols as well as APIs to parse and write X.509, PKCS #12, OpenPGP and other required structures. It is aimed to be portable and efficient with focus on security and interoperability. *homepage*: http://www.gnutls.org/ ========== ================== version toolchain ========== ================== ``3.3.21`` ``intel/2016a`` ``3.4.7`` ``GNU/4.9.3-2.25`` ``3.4.11`` ``foss/2016a`` ========== ================== .. _list_software_Go_182: *Go* ++++ Go is an open source programming language that makes it easy to build simple, reliable, and efficient software. *homepage*: http://www.golang.org ========== ================= version toolchain ========== ================= ``1.2.1`` ``GCC/4.8.2`` ``1.4.2`` ``GCC/4.8.4`` ``1.5`` ``GCC/4.8.4`` ``1.8.1`` ``system`` ``1.11.5`` ``system`` ``1.12`` ``system`` ``1.12.1`` ``GCCcore/7.3.0`` ``1.13.1`` ``system`` ========== ================= .. _list_software_GObject-Introspection_2108: *GObject-Introspection* +++++++++++++++++++++++ GObject introspection is a middleware layer between C libraries (using GObject) and language bindings. The C library can be scanned at compile time and generate a metadata file, in addition to the actual native C library. Then at runtime, language bindings can read this metadata and automatically provide bindings to call into the C library. *homepage*: https://wiki.gnome.org/GObjectIntrospection/ ========== ================== ================================== version versionsuffix toolchain ========== ================== ================================== ``1.47.1`` ``foss/2016a``, ``intel/2016a`` ``1.48.0`` ``foss/2016a``, ``intel/2016a`` ``1.49.1`` ``foss/2016b``, ``intel/2016b`` ``1.52.0`` ``intel/2017a`` ``1.53.5`` ``-Python-2.7.13`` ``intel/2017a`` ``1.53.5`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.53.5`` ``-Python-3.6.1`` ``intel/2017a`` ``1.54.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``1.54.1`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` ``1.54.1`` ``-Python-3.6.6`` ``fosscuda/2018b`` ``1.60.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================== ================================== .. _list_software_golf_424: *golf* ++++++ GNU Compiler Collection (GCC) based compiler toolchain, including OpenBLAS (BLAS and LAPACK support) and FFTW. *homepage*: (none) ========= ========== version toolchain ========= ========== ``2018a`` ``system`` ========= ========== .. _list_software_gomkl_538: *gomkl* +++++++ GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL *homepage*: (none) ========= ========== version toolchain ========= ========== ``2018b`` ``system`` ``2019a`` ``system`` ========= ========== .. _list_software_gompi_540: *gompi* +++++++ GNU Compiler Collection (GCC) based compiler toolchain, including OpenMPI for MPI support. *homepage*: (none) =========== ============= ========== version versionsuffix toolchain =========== ============= ========== ``2016.04`` ``system`` ``2016.06`` ``system`` ``2016.07`` ``system`` ``2016.09`` ``system`` ``2016a`` ``system`` ``2016b`` ``system`` ``2017a`` ``system`` ``2017b`` ``system`` ``2018.08`` ``system`` ``2018a`` ``system`` ``2018b`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` ``system`` ``-2.29`` ``system`` =========== ============= ========== .. _list_software_gompic_639: *gompic* ++++++++ GNU Compiler Collection (GCC) based compiler toolchain along with CUDA toolkit, including OpenMPI for MPI support with CUDA features enabled. *homepage*: (none) ========= ========== version toolchain ========= ========== ``2017b`` ``system`` ``2018a`` ``system`` ``2018b`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` ========= ========== .. _list_software_google-java-format_1794: *google-java-format* ++++++++++++++++++++ Reformats Java source code to comply with Google Java Style. *homepage*: https://github.com/google/google-java-format ======= ============= ========== version versionsuffix toolchain ======= ============= ========== ``1.7`` ``-Java-1.8`` ``system`` ======= ============= ========== .. _list_software_googletest_1085: *googletest* ++++++++++++ Google's C++ test framework *homepage*: https://github.com/google/googletest ========= ===================================================================== version toolchain ========= ===================================================================== ``1.8.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b`` ========= ===================================================================== .. _list_software_GP2C_268: *GP2C* ++++++ The gp2c compiler is a package for translating GP routines into the C programming language, so that they can be compiled and used with the PARI system or the GP calculator. *homepage*: http://pari.math.u-bordeaux.fr/pub/pari/manuals/gp2c/gp2c.html ============ ============== version toolchain ============ ============== ``0.0.9pl5`` ``foss/2016a`` ============ ============== .. _list_software_GPAW_303: *GPAW* ++++++ GPAW is a density-functional theory (DFT) Python code based on the projector-augmented wave (PAW) method and the atomic simulation environment (ASE). It uses real-space uniform grids and multigrid methods or atom-centered basis-functions. *homepage*: https://wiki.fysik.dtu.dk/gpaw/ ========== ============================ =============================== version versionsuffix toolchain ========== ============================ =============================== ``1.4.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``19.8.1`` ``-ASE-3.18.0-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``19.8.1`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ========== ============================ =============================== .. _list_software_GPAW-setups_1024: *GPAW-setups* +++++++++++++ PAW setup for the GPAW Density Functional Theory package. Users can install setups manually using 'gpaw install-data' or use setups from this package. The versions of GPAW and GPAW-setups can be intermixed. *homepage*: https://wiki.fysik.dtu.dk/gpaw/ ============= ========== version toolchain ============= ========== ``0.8.7929`` ``system`` ``0.9.9672`` ``system`` ``0.9.11271`` ``system`` ``0.9.20000`` ``system`` ============= ========== .. _list_software_gperf_532: *gperf* +++++++ GNU gperf is a perfect hash function generator. For a given list of strings, it produces a hash function and hash table, in form of C or C++ code, for looking up a value depending on the input string. The hash function is perfect, which means that the hash table has no collisions, and the hash table lookup needs a single string comparison only. *homepage*: https://www.gnu.org/software/gperf/ ========= ========================================================================================================================= version toolchain ========= ========================================================================================================================= ``3.0.4`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``3.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ========================================================================================================================= .. _list_software_gperftools_1093: *gperftools* ++++++++++++ gperftools are for use by developers so that they can create more robust applications. Especially of use to those developing multi-threaded applications in C++ with templates. Includes TCMalloc, heap-checker, heap-profiler and cpu-profiler. *homepage*: http://github.com/gperftools/gperftools ========= =============================== version toolchain ========= =============================== ``2.5`` ``foss/2016a``, ``intel/2016b`` ``2.6.3`` ``GCCcore/6.4.0`` ========= =============================== .. _list_software_gpustat_776: *gpustat* +++++++++ dstat-like utilization monitor for NVIDIA GPUs *homepage*: https://github.com/wookayin/gpustat ========= ================== ================== version versionsuffix toolchain ========= ================== ================== ``0.5.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` ========= ================== ================== .. _list_software_Grace_482: *Grace* +++++++ Grace is a WYSIWYG tool to make two-dimensional plots of numerical data. *homepage*: http://plasma-gate.weizmann.ac.il/Grace/ ========== ============= =============================================== version versionsuffix toolchain ========== ============= =============================================== ``5.1.25`` ``-5build1`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` ========== ============= =============================================== .. _list_software_grace_514: *grace* +++++++ Grace is a WYSIWYG 2D plotting tool for X Windows System and Motif. *homepage*: http://freecode.com/projects/grace ========== =============================== version toolchain ========== =============================== ``5.1.25`` ``foss/2016a``, ``intel/2016a`` ========== =============================== .. _list_software_Gradle_591: *Gradle* ++++++++ Complete Gradle install. From mobile apps to microservices, from small startups to big enterprises, Gradle helps teams build, automate and deliver better software, faster. *homepage*: https://gradle.org ========= ========== version toolchain ========= ========== ``4.5.1`` ``system`` ========= ========== .. _list_software_gradunwarp_1083: *gradunwarp* ++++++++++++ Gradient Unwarping. This is the Human Connectome Project fork of the no longer maintained original. *homepage*: https://github.com/Washington-University/gradunwarp ========= ====================== ============== version versionsuffix toolchain ========= ====================== ============== ``1.1.0`` ``-HCP-Python-2.7.15`` ``foss/2019a`` ========= ====================== ============== .. _list_software_graph-tool_1021: *graph-tool* ++++++++++++ Graph-tool is an efficient Python module for manipulation and statistical analysis of graphs (a.k.a. networks). Contrary to most other python modules with similar functionality, the core data structures and algorithms are implemented in C++, making extensive use of template metaprogramming, based heavily on the Boost Graph Library. This confers it a level of performance that is comparable (both in memory usage and computation time) to that of a pure C/C++ library. *homepage*: https://graph-tool.skewed.de/ ======== ================= ============== version versionsuffix toolchain ======== ================= ============== ``2.26`` ``-Python-3.6.3`` ``foss/2017b`` ``2.27`` ``-Python-3.6.6`` ``foss/2018b`` ======== ================= ============== .. _list_software_Graphene_810: *Graphene* ++++++++++ Graphene is a a thin layer of types for graphic libraries *homepage*: https://ebassi.github.io/graphene/ ========= =============== version toolchain ========= =============== ``1.6.0`` ``intel/2017a`` ========= =============== .. _list_software_GraphicsMagick_1405: *GraphicsMagick* ++++++++++++++++ GraphicsMagick is the swiss army knife of image processing. *homepage*: http://www.graphicsmagick.org/ ========== ================================ version toolchain ========== ================================ ``1.3.23`` ``foss/2016a``, ``intel/2016a`` ``1.3.25`` ``intel/2016b``, ``intel/2017a`` ``1.3.28`` ``foss/2018a`` ``1.3.31`` ``foss/2018b`` ========== ================================ .. _list_software_Graphviz_843: *Graphviz* ++++++++++ Graphviz is open source graph visualization software. Graph visualization is a way of representing structural information as diagrams of abstract graphs and networks. It has important applications in networking, bioinformatics, software engineering, database and web design, machine learning, and in visual interfaces for other technical domains. *homepage*: http://www.graphviz.org/ ========== =============================== version toolchain ========== =============================== ``2.38.0`` ``foss/2016b``, ``intel/2016b`` ``2.40.1`` ``intel/2018a`` ========== =============================== .. _list_software_graphviz_875: *graphviz* ++++++++++ Simple Python interface for Graphviz *homepage*: https://pypi.python.org/pypi/graphviz ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``0.5.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``0.5.1`` ``-Python-3.5.2`` ``intel/2016b`` ``0.8.2`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================== =============================== .. _list_software_GRASS_384: *GRASS* +++++++ The Geographic Resources Analysis Support System - used for geospatial data management and analysis, image processing, graphics and maps production, spatial modeling, and visualization *homepage*: http://grass.osgeo.org ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``7.6.0`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== ============== .. _list_software_Greenlet_822: *Greenlet* ++++++++++ The greenlet package is a spin-off of Stackless, a version of CPython that supports micro-threads called "tasklets". Tasklets run pseudo-concurrently (typically in a single or a few OS-level threads) and are synchronized with data exchanges on "channels". A "greenlet", on the other hand, is a still more primitive notion of micro-thread with no implicit scheduling; coroutines, in other words. This is useful when you want to control exactly when your code runs. *homepage*: https://github.com/python-greenlet/greenlet ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``0.4.9`` ``-Python-2.7.11`` ``intel/2016a`` ``0.4.9`` ``-Python-3.5.1`` ``intel/2016a`` ``0.4.11`` ``-Python-2.7.12`` ``intel/2016b`` ``0.4.12`` ``-Python-2.7.14`` ``intel/2017b`` ========== ================== =============== .. _list_software_Grep_398: *Grep* ++++++ The grep command searches one or more input files for lines containing a match to a specified pattern. By default, grep prints the matching lines. *homepage*: http://www.gnu.org/software/grep/ ======== ============= version toolchain ======== ============= ``2.21`` ``GCC/4.9.2`` ======== ============= .. _list_software_grib_api_829: *grib_api* ++++++++++ The ECMWF GRIB API is an application program interface accessible from C, FORTRAN and Python programs developed for encoding and decoding WMO FM-92 GRIB edition 1 and edition 2 messages. A useful set of command line tools is also provided to give quick access to GRIB messages. *homepage*: https://software.ecmwf.int/wiki/display/GRIB/Home ========== ================================================ version toolchain ========== ================================================ ``1.16.0`` ``intel/2016a`` ``1.21.0`` ``foss/2017a`` ``1.24.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ========== ================================================ .. _list_software_GRIT_310: *GRIT* ++++++ GRIT - A tool for the integrative analysis of RNA-seq type assays *homepage*: https://github.com/nboley/grit ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``2.0.5`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== .. _list_software_GRNBoost_750: *GRNBoost* ++++++++++ XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable. *homepage*: https://github.com/dmlc/xgboost ============ =================== =============== version versionsuffix toolchain ============ =================== =============== ``20171009`` ``-Java-1.8.0_152`` ``intel/2017b`` ============ =================== =============== .. _list_software_GroIMP_526: *GroIMP* ++++++++ GroIMP (Growth Grammar-related Interactive Modelling Platform) is a 3D-modelling platform. *homepage*: http://www.grogra.de/software/groimp ======= ========== version toolchain ======= ========== ``1.5`` ``system`` ======= ========== .. _list_software_GROMACS_524: *GROMACS* +++++++++ GROMACS is a versatile package to perform molecular dynamics, i.e. simulate the Newtonian equations of motion for systems with hundreds to millions of particles. *homepage*: http://www.gromacs.org ========== ================= ============================================================================================================ version versionsuffix toolchain ========== ================= ============================================================================================================ ``5.1.2`` ``-hybrid`` ``foss/2016a``, ``intel/2016a`` ``5.1.2`` ``-hybrid-dp`` ``intel/2016a`` ``5.1.2`` ``-mt`` ``foss/2016a`` ``5.1.4`` ``-hybrid`` ``foss/2016b`` ``5.1.4`` ``-mt`` ``foss/2016b`` ``2016`` ``-hybrid`` ``foss/2016b`` ``2016`` ``-mt`` ``foss/2016b`` ``2016.1`` ``-PLUMED`` ``foss/2017a`` ``2016.2`` ``foss/2017a`` ``2016.3`` ``foss/2017a``, ``intel/2017a`` ``2016.3`` ``-GPU-enabled`` ``foss/2016b`` ``2016.4`` ``foss/2017b``, ``fosscuda/2017b``, ``giolf/2017b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` ``2016.5`` ``intel/2018a`` ``2018`` ``foss/2018a`` ``2018.1`` ``-PLUMED`` ``foss/2018b`` ``2018.2`` ``foss/2017b``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018b``, ``intel/2017b``, ``intelcuda/2017b`` ``2018.3`` ``foss/2018b``, ``fosscuda/2018b`` ``2018.4`` ``-PLUMED-2.5.0`` ``foss/2018b``, ``fosscuda/2018b`` ``2019`` ``foss/2018b``, ``fosscuda/2018b`` ``2019.2`` ``fosscuda/2019a`` ``2019.3`` ``foss/2019a``, ``foss/2019b``, ``fosscuda/2019a``, ``fosscuda/2019b`` ``2019.4`` ``foss/2019b`` ========== ================= ============================================================================================================ .. _list_software_GromacsWrapper_1453: *GromacsWrapper* ++++++++++++++++ GromacsWrapper is a python package that wraps system calls to Gromacs tools into thin classes. This allows for fairly seamless integration of the gromacs tools into python scripts. *homepage*: https://gromacswrapper.readthedocs.org ========= ================= ================== version versionsuffix toolchain ========= ================= ================== ``0.8.0`` ``-Python-3.7.2`` ``fosscuda/2019a`` ========= ================= ================== .. _list_software_GroopM_596: *GroopM* ++++++++ GroopM is a metagenomic binning toolset. It leverages spatio-temporal dynamics (differential coverage) to accurately (and almost automatically) extract population genomes from multi-sample metagenomic datasets. *homepage*: http://ecogenomics.github.io/GroopM/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``0.3.4`` ``-Python-2.7.12`` ``foss/2016b`` ========= ================== ============== .. _list_software_gsettings-desktop-schemas_2576: *gsettings-desktop-schemas* +++++++++++++++++++++++++++ gsettings-desktop-schemas contains a collection of GSettings schemas for settings shared by various components of a desktop. *homepage*: https://gitlab.gnome.org/GNOME/gsettings-desktop-schemas ========== ================= version toolchain ========== ================= ``3.34.0`` ``GCCcore/8.2.0`` ========== ================= .. _list_software_GSL_230: *GSL* +++++ The GNU Scientific Library (GSL) is a numerical library for C and C++ programmers. The library provides a wide range of mathematical routines such as random number generators, special functions and least-squares fitting. *homepage*: https://www.gnu.org/software/gsl/ ========= ============================================================================================================================ version toolchain ========= ============================================================================================================================ ``1.16`` ``foss/2016a``, ``intel/2016a`` ``2.1`` ``GCC/5.4.0-2.26``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` ``2.2.1`` ``intel/2016a``, ``intel/2016b`` ``2.3`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b``, ``intel/2017a`` ``2.4`` ``GCCcore/6.4.0`` ``2.5`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``iccifort/2018.3.222-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2.6`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ========= ============================================================================================================================ .. _list_software_gSOAP_410: *gSOAP* +++++++ The gSOAP toolkit is a C and C++ software development toolkit for SOAP and REST XML Web services and generic C/C++ XML data bindings. The toolkit analyzes WSDLs and XML schemas (separately or as a combined set) and maps the XML schema types and the SOAP/REST XML messaging protocols to easy-to-use and efficient C and C++ code. It also supports exposing (legacy) C and C++ applications as XML Web services by auto-generating XML serialization code and WSDL specifications. Or you can simply use it to automatically convert XML to/from C and C++ data. The toolkit supports options to generate pure ANSI C or C++ with or without STL. *homepage*: http://www.cs.fsu.edu/~engelen/soap.html ========== ================= version toolchain ========== ================= ``2.8.48`` ``GCCcore/6.3.0`` ========== ================= .. _list_software_GST-plugins-base_1509: *GST-plugins-base* ++++++++++++++++++ GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. *homepage*: https://gstreamer.freedesktop.org/ =========== ================================================================================================================== version toolchain =========== ================================================================================================================== ``0.10.36`` ``foss/2016a``, ``foss/2017b``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``1.6.4`` ``foss/2016a`` ``1.8.3`` ``foss/2016a`` ``1.16.0`` ``GCC/8.2.0-2.31.1`` =========== ================================================================================================================== .. _list_software_GStreamer_906: *GStreamer* +++++++++++ GStreamer is a library for constructing graphs of media-handling components. The applications it supports range from simple Ogg/Vorbis playback, audio/video streaming to complex audio (mixing) and video (non-linear editing) processing. *homepage*: https://gstreamer.freedesktop.org/ =========== ================================================================================================================== version toolchain =========== ================================================================================================================== ``0.10.36`` ``foss/2016a``, ``foss/2017b``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``1.6.4`` ``foss/2016a`` ``1.8.3`` ``foss/2016a`` ``1.15.1`` ``fosscuda/2018b`` ``1.16.0`` ``GCC/8.2.0-2.31.1`` =========== ================================================================================================================== .. _list_software_GTDB-Tk_525: *GTDB-Tk* +++++++++ A toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes. *homepage*: https://github.com/Ecogenomics/GTDBTk ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``0.2.2`` ``-Python-2.7.15`` ``intel/2018b`` ``0.3.2`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ========= ================== =============================== .. _list_software_gtest_551: *gtest* +++++++ Google's framework for writing C++ tests on a variety of platforms *homepage*: https://github.com/google/googletest ========= ==================================== version toolchain ========= ==================================== ``1.8.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.8.1`` ``GCCcore/8.2.0`` ========= ==================================== .. _list_software_GTK+_273: *GTK+* ++++++ The GTK+ 2 package contains libraries used for creating graphical user interfaces for applications. *homepage*: https://developer.gnome.org/gtk+/stable/ =========== ================================================================================ version toolchain =========== ================================================================================ ``2.24.28`` ``intel/2016a`` ``2.24.30`` ``foss/2016a``, ``intel/2016a`` ``2.24.31`` ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` ``2.24.32`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ``3.22.30`` ``fosscuda/2018b`` ``3.24.8`` ``GCCcore/8.2.0`` =========== ================================================================================ .. _list_software_GtkSourceView_1330: *GtkSourceView* +++++++++++++++ GtkSourceView is a GNOME library that extends GtkTextView, the standard GTK+ widget for multiline text editing. GtkSourceView adds support for syntax highlighting, undo/redo, file loading and saving, search and replace, a completion system, printing, displaying line numbers, and other features typical of a source code editor. *homepage*: https://wiki.gnome.org/Projects/GtkSourceView =========== ================= version toolchain =========== ================= ``3.24.11`` ``GCCcore/8.2.0`` ``4.4.0`` ``GCCcore/8.2.0`` =========== ================= .. _list_software_GTOOL_389: *GTOOL* +++++++ GTOOL is a program for transforming sets of genotype data for use with the programs SNPTEST and IMPUTE. *homepage*: http://www.well.ox.ac.uk/~cfreeman/software/gwas/gtool.html ========= ========== version toolchain ========= ========== ``0.7.5`` ``system`` ========= ========== .. _list_software_GTS_238: *GTS* +++++ GTS stands for the GNU Triangulated Surface Library. It is an Open Source Free Software Library intended to provide a set of useful functions to deal with 3D surfaces meshed with interconnected triangles. *homepage*: http://gts.sourceforge.net/ ============ ================================================================================================================= version toolchain ============ ================================================================================================================= ``0.7.6`` ``foss/2016a``, ``foss/2016b``, ``foss/2018b``, ``foss/2019b``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` ``20121130`` ``foss/2017b`` ============ ================================================================================================================= .. _list_software_guenomu_768: *guenomu* +++++++++ guenomu is a software written in C that estimates the species tree for a given set of gene families. *homepage*: https://bitbucket.org/leomrtns/guenomu ============== ============= =============== version versionsuffix toolchain ============== ============= =============== ``2019.07.05`` ``-mpi`` ``iimpi/2019a`` ============== ============= =============== .. _list_software_Guile_502: *Guile* +++++++ Guile is a programming language, designed to help programmers create flexible applications that can be extended by users or other programmers with plug-ins, modules, or scripts. *homepage*: https://www.gnu.org/software/guile/ ========== =================================================================================================================================================================================================== version toolchain ========== =================================================================================================================================================================================================== ``1.8.8`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b`` ``2.0.11`` ``GCC/4.9.3-2.25``, ``foss/2016a`` ``2.2.2`` ``GCCcore/6.4.0`` ``2.2.4`` ``GCCcore/7.3.0`` ========== =================================================================================================================================================================================================== .. _list_software_GULP_312: *GULP* ++++++ GULP is a program for performing a variety of types of simulation on materials using boundary conditions of 0-D (molecules and clusters), 1-D (polymers), 2-D (surfaces, slabs and grain boundaries), or 3-D (periodic solids)Band Unfolding code for Plane-wave based calculations *homepage*: https://gulp.curtin.edu.au/gulp/ ======= =============== version toolchain ======= =============== ``5.1`` ``intel/2019a`` ======= =============== .. _list_software_Gurobi_616: *Gurobi* ++++++++ The Gurobi Optimizer is a state-of-the-art solver for mathematical programming. The solvers in the Gurobi Optimizer were designed from the ground up to exploit modern architectures and multi-core processors, using the most advanced implementations of the latest algorithms. *homepage*: https://www.gurobi.com ========= ================= =============================== version versionsuffix toolchain ========= ================= =============================== ``6.5.1`` ``system`` ``6.5.2`` ``system`` ``7.0.1`` ``system`` ``7.5.2`` ``system`` ``7.5.2`` ``-Python-3.6.4`` ``intel/2018a`` ``8.1.1`` ``system`` ``9.0.0`` ``system`` ``9.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ========= ================= =============================== .. _list_software_gzip_442: *gzip* ++++++ gzip (GNU zip) is a popular data compression program as a replacement for compress *homepage*: http://www.gnu.org/software/gzip/ ======== ======================================================= version toolchain ======== ======================================================= ``1.8`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.9`` ``GCCcore/7.3.0`` ``1.10`` ``GCCcore/8.2.0`` ======== ======================================================= .. _list_software_letter_h: *H* --- :ref:`list_software_h4toh5_540` - :ref:`list_software_H5hut_462` - :ref:`list_software_h5py_390` - :ref:`list_software_Hadoop_603` - :ref:`list_software_hanythingondemand_1808` - :ref:`list_software_HAPGEN2_485` - :ref:`list_software_HarfBuzz_812` - :ref:`list_software_Harminv_725` - :ref:`list_software_HBase_451` - :ref:`list_software_HDDM_285` - :ref:`list_software_HDF_210` - :ref:`list_software_HDF5_263` - :ref:`list_software_hdf5storage_1116` - :ref:`list_software_HDFView_621` - :ref:`list_software_HEALPix_587` - :ref:`list_software_heaptrack_947` - :ref:`list_software_Hello_500` - :ref:`list_software_help2man_791` - :ref:`list_software_HH-suite_743` - :ref:`list_software_HiC-Pro_594` - :ref:`list_software_HiCExplorer_1093` - :ref:`list_software_HIPS_308` - :ref:`list_software_HISAT2_427` - :ref:`list_software_HLAminer_752` - :ref:`list_software_HMMER_377` - :ref:`list_software_hmmlearn_852` - :ref:`list_software_HOME_297` - :ref:`list_software_Horovod_737` - :ref:`list_software_horton_666` - :ref:`list_software_HPCG_290` - :ref:`list_software_HPCX_307` - :ref:`list_software_HPDBSCAN_579` - :ref:`list_software_HPL_228` - :ref:`list_software_htop_443` - :ref:`list_software_HTSeq_453` - :ref:`list_software_HTSlib_550` - :ref:`list_software_hub_319` - :ref:`list_software_hunspell_875` - :ref:`list_software_hwloc_541` - :ref:`list_software_Hyperopt_859` - :ref:`list_software_hyperspy_900` - :ref:`list_software_HyPhy_498` - :ref:`list_software_hypothesis_1104` - :ref:`list_software_Hypre_520` .. _list_software_h4toh5_540: *h4toh5* ++++++++ The h4toh5 software consists of the h4toh5 and h5toh4 command-line utilities, as well as a conversion library for converting between individual HDF4 and HDF5 objects. *homepage*: http://www.hdfgroup.org/h4toh5/ ========= ======================== ========== version versionsuffix toolchain ========= ======================== ========== ``2.2.2`` ``-linux-x86_64-static`` ``system`` ========= ======================== ========== .. _list_software_H5hut_462: *H5hut* +++++++ HDF5 Utility Toolkit: High-Performance I/O Library for Particle-based Simulations *homepage*: https://amas.psi.ch/H5hut/ =========== =============== version toolchain =========== =============== ``1.99.13`` ``intel/2016b`` =========== =============== .. _list_software_h5py_390: *h5py* ++++++ HDF5 for Python (h5py) is a general-purpose Python interface to the Hierarchical Data Format library, version 5. HDF5 is a versatile, mature scientific software library designed for the fast, flexible storage of enormous amounts of data. *homepage*: http://www.h5py.org/ ========== ===================================== ==================================================================================== version versionsuffix toolchain ========== ===================================== ==================================================================================== ``2.5.0`` ``-Python-2.7.11-HDF5-1.8.16`` ``foss/2016a``, ``intel/2016a`` ``2.5.0`` ``-Python-2.7.11-HDF5-1.8.16-serial`` ``foss/2016a``, ``intel/2016a`` ``2.5.0`` ``-Python-3.5.1-HDF5-1.8.16`` ``foss/2016a`` ``2.6.0`` ``-Python-2.7.11`` ``intel/2016a`` ``2.6.0`` ``-Python-2.7.12-HDF5-1.10.0-patch1`` ``foss/2016b``, ``intel/2016b`` ``2.6.0`` ``-Python-2.7.12-HDF5-1.8.17`` ``foss/2016b``, ``intel/2016b`` ``2.6.0`` ``-Python-2.7.12-HDF5-1.8.18`` ``foss/2016b``, ``intel/2016b`` ``2.6.0`` ``-Python-3.5.2-HDF5-1.10.0-patch1`` ``foss/2016b``, ``intel/2016b`` ``2.6.0`` ``-Python-3.5.2-HDF5-1.8.17`` ``intel/2016b`` ``2.6.0`` ``-Python-3.5.2-HDF5-1.8.18`` ``foss/2016b``, ``intel/2016b`` ``2.7.0`` ``-Python-2.7.12`` ``intel/2016b`` ``2.7.0`` ``-Python-2.7.13`` ``intel/2017a`` ``2.7.0`` ``-Python-2.7.13-HDF5-1.10.1`` ``foss/2017a`` ``2.7.0`` ``-Python-2.7.13-HDF5-1.8.19`` ``foss/2017a`` ``2.7.0`` ``-Python-3.6.1`` ``intel/2017a`` ``2.7.0`` ``-Python-3.6.1-HDF5-1.10.0-patch1`` ``intel/2017a`` ``2.7.0`` ``-Python-3.6.1-HDF5-1.10.1`` ``foss/2017a`` ``2.7.0`` ``-Python-3.6.1-HDF5-1.8.19`` ``foss/2017a`` ``2.7.1`` ``-Python-2.7.13`` ``intel/2017a`` ``2.7.1`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018a`` ``2.7.1`` ``-Python-2.7.14-serial`` ``intel/2018a`` ``2.7.1`` ``-Python-3.6.1`` ``intel/2017a`` ``2.7.1`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b`` ``2.7.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``2.8.0`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.8.0`` ``-Python-2.7.15-serial`` ``intel/2018b`` ``2.8.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.9.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` ``2.10.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` ========== ===================================== ==================================================================================== .. _list_software_Hadoop_603: *Hadoop* ++++++++ Hadoop MapReduce by Cloudera *homepage*: https://archive.cloudera.com/cdh5/cdh/5/ =================== ========================== ================= version versionsuffix toolchain =================== ========================== ================= ``2.4.0`` ``-seagate-722af1-native`` ``system`` ``2.5.0-cdh5.3.1`` ``-native`` ``system`` ``2.6.0-cdh5.4.5`` ``-native`` ``system`` ``2.6.0-cdh5.7.0`` ``-native`` ``system`` ``2.6.0-cdh5.8.0`` ``-native`` ``system`` ``2.6.0-cdh5.12.0`` ``-native`` ``system`` ``2.9.2`` ``-native`` ``GCCcore/7.3.0`` =================== ========================== ================= .. _list_software_hanythingondemand_1808: *hanythingondemand* +++++++++++++++++++ HanythingOnDemand (HOD) is a system for provisioning virtual Hadoop clusters over a large physical cluster. It uses the Torque resource manager to do node allocation. *homepage*: https://github.com/hpcugent/hanythingondemand ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``3.0.0`` ``-cli`` ``system`` ``3.0.1`` ``-cli`` ``system`` ``3.0.2`` ``-cli`` ``system`` ``3.0.3`` ``-cli`` ``system`` ``3.0.4`` ``-cli`` ``system`` ``3.1.0`` ``-Python-2.7.11`` ``intel/2016a`` ``3.1.0`` ``-cli`` ``system`` ``3.1.1`` ``-Python-2.7.11`` ``intel/2016a`` ``3.1.1`` ``-cli`` ``system`` ``3.1.2`` ``-Python-2.7.11`` ``intel/2016a`` ``3.1.2`` ``-cli`` ``system`` ``3.1.3`` ``-Python-2.7.12`` ``intel/2016b`` ``3.1.3`` ``-cli`` ``system`` ``3.1.4`` ``-Python-2.7.12`` ``intel/2016b`` ``3.1.4`` ``-cli`` ``system`` ``3.2.0`` ``-Python-2.7.12`` ``intel/2016b`` ``3.2.0`` ``-cli`` ``system`` ``3.2.2`` ``-Python-2.7.12`` ``intel/2016b`` ``3.2.2`` ``-cli`` ``system`` ========= ================== =============== .. _list_software_HAPGEN2_485: *HAPGEN2* +++++++++ 'HAPGEN2' simulates case control datasets at SNP markers. *homepage*: https://mathgen.stats.ox.ac.uk/genetics_software/hapgen/hapgen2.html ========= ========== version toolchain ========= ========== ``2.2.0`` ``system`` ========= ========== .. _list_software_HarfBuzz_812: *HarfBuzz* ++++++++++ HarfBuzz is an OpenType text shaping engine. *homepage*: https://www.freedesktop.org/wiki/Software/HarfBuzz ========= ================================================ version toolchain ========= ================================================ ``1.1.3`` ``foss/2016a``, ``intel/2016a`` ``1.2.7`` ``foss/2016a``, ``intel/2016a`` ``1.3.1`` ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` ``1.5.1`` ``intel/2017a`` ``1.7.1`` ``foss/2017b``, ``intel/2017b`` ``1.7.5`` ``foss/2018a``, ``intel/2018a`` ``1.9.0`` ``fosscuda/2018b`` ``2.2.0`` ``foss/2018b``, ``fosscuda/2018b`` ``2.4.0`` ``GCCcore/8.2.0`` ========= ================================================ .. _list_software_Harminv_725: *Harminv* +++++++++ Harminv is a free program (and accompanying library) to solve the problem of harmonic inversion - given a discrete-time, finite-length signal that consists of a sum of finitely-many sinusoids (possibly exponentially decaying) in a given bandwidth, it determines the frequencies, decay constants, amplitudes, and phases of those sinusoids. *homepage*: http://ab-initio.mit.edu/wiki/index.php/Harminv ======= ============== version toolchain ======= ============== ``1.4`` ``foss/2016a`` ======= ============== .. _list_software_HBase_451: *HBase* +++++++ Apache HBase. is the Hadoop database, a distributed, scalable, big data store. *homepage*: http://hbase.apache.org/ ========= ========== version toolchain ========= ========== ``1.0.2`` ``system`` ========= ========== .. _list_software_HDDM_285: *HDDM* ++++++ HDDM is a Puthon toolbox for hierarchical Bayesian parameter estimation of the Drift Diffusion Model (via PyMC). *homepage*: http://ski.clps.brown.edu/hddm_docs ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``0.6.1`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================= =============== .. _list_software_HDF_210: *HDF* +++++ HDF (also known as HDF4) is a library and multi-object file format for storing and managing data between machines. *homepage*: https://www.hdfgroup.org/products/hdf4/ ========== ============== ========================================================================== version versionsuffix toolchain ========== ============== ========================================================================== ``4.2.11`` ``intel/2016a`` ``4.2.12`` ``intel/2017a`` ``4.2.13`` ``GCCcore/6.4.0`` ``4.2.13`` ``-no-netcdf`` ``intel/2017a`` ``4.2.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========== ============== ========================================================================== .. _list_software_HDF5_263: *HDF5* ++++++ HDF5 is a data model, library, and file format for storing and managing data. It supports an unlimited variety of datatypes, and is designed for flexible and efficient I/O and for high volume and complex data. *homepage*: https://portal.hdfgroup.org/display/support ================= ============= ================================================================================================================================================================================================================== version versionsuffix toolchain ================= ============= ================================================================================================================================================================================================================== ``1.8.10`` ``-serial`` ``GCC/4.8.1`` ``1.8.11`` ``-serial`` ``GCC/4.8.1`` ``1.8.12`` ``foss/2018b``, ``intel/2016b`` ``1.8.13`` ``foss/2018b`` ``1.8.16`` ``foss/2016a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``1.8.16`` ``-serial`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``1.8.17`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.8.17`` ``-serial`` ``GCC/5.4.0-2.26``, ``foss/2016a``, ``intel/2016b`` ``1.8.18`` ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a`` ``1.8.18`` ``-serial`` ``intel/2017a`` ``1.8.19`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``1.8.20`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``1.10.0-patch1`` ``foss/2016b``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a`` ``1.10.1`` ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018a``, ``intelcuda/2017b``, ``iomkl/2017b``, ``iomkl/2018a`` ``1.10.2`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``1.10.5`` ``gompi/2019a``, ``gompi/2019b``, ``gompic/2019a``, ``gompic/2019b``, ``iimpi/2019a``, ``iimpi/2019b``, ``iimpic/2019a``, ``iimpic/2019b`` ================= ============= ================================================================================================================================================================================================================== .. _list_software_hdf5storage_1116: *hdf5storage* +++++++++++++ This Python package provides high level utilities to read/write a variety of Python types to/from HDF5 (Heirarchal Data Format) formatted files. This package also provides support for MATLAB MAT v7.3 formatted files, which are just HDF5 files with a different extension and some extra meta-data. All of this is done without pickling data. Pickling is bad for security because it allows arbitrary code to be executed in the interpreter. One wants to be able to read possibly HDF5 and MAT files from untrusted sources, so pickling is avoided in this package. *homepage*: https://pythonhosted.org/hdf5storage/ ========== ================================== version toolchain ========== ================================== ``0.1.15`` ``foss/2019a``, ``fosscuda/2019a`` ========== ================================== .. _list_software_HDFView_621: *HDFView* +++++++++ HDFView is a visual tool for browsing and editing HDF4 and HDF5 files. *homepage*: https://support.hdfgroup.org/products/java/hdfview/ ======== =========================== ========== version versionsuffix toolchain ======== =========================== ========== ``2.14`` ``-Java-1.8.0_152-centos6`` ``system`` ``2.14`` ``-Java-1.8.0_152-centos7`` ``system`` ======== =========================== ========== .. _list_software_HEALPix_587: *HEALPix* +++++++++ Hierarchical Equal Area isoLatitude Pixelation of a sphere. *homepage*: http://healpix.sourceforge.net/ ======== ==================================== version toolchain ======== ==================================== ``3.50`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ======== ==================================== .. _list_software_heaptrack_947: *heaptrack* +++++++++++ A heap memory profiler for Linux. *homepage*: http://milianw.de/blog/heaptrack-a-heap-memory-profiler-for-linux ========= ============== version toolchain ========= ============== ``1.1.0`` ``foss/2016b`` ========= ============== .. _list_software_Hello_500: *Hello* +++++++ The GNU Hello program produces a familiar, friendly greeting. Yes, this is another implementation of the classic program that prints "Hello, world!" when you run it. However, unlike the minimal version often seen, GNU Hello processes its argument list to modify its behavior, supports greetings in many languages, and so on. *homepage*: https://www.gnu.org/software/hello/ ======== ================= version toolchain ======== ================= ``2.10`` ``GCCcore/8.2.0`` ======== ================= .. _list_software_help2man_791: *help2man* ++++++++++ help2man produces simple manual pages from the '--help' and '--version' output of other commands. *homepage*: https://www.gnu.org/software/help2man/ =========== ================================================================================================================================================================================== version toolchain =========== ================================================================================================================================================================================== ``1.47.4`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/system``, ``gimkl/2017a``, ``intel/2016b``, ``system`` ``1.47.5`` ``GCCcore/5.5.0`` ``1.47.6`` ``GCCcore/8.1.0`` ``1.47.7`` ``GCCcore/8.2.0`` ``1.47.8`` ``GCCcore/7.4.0``, ``GCCcore/8.3.0`` ``1.47.10`` ``GCCcore/9.1.0``, ``GCCcore/9.2.0`` =========== ================================================================================================================================================================================== .. _list_software_HH-suite_743: *HH-suite* ++++++++++ HH-suite is an open-source software package for sensitive protein sequence searching. It contains programs that can search for similar protein sequences in protein sequence databases. *homepage*: https://github.com/soedinglab/hh-suite ============== =============== version toolchain ============== =============== ``3.0-beta.3`` ``intel/2018a`` ``3.2.0`` ``foss/2019b`` ============== =============== .. _list_software_HiC-Pro_594: *HiC-Pro* +++++++++ HiC-Pro was designed to process Hi-C data, from raw fastq files (paired-end Illumina data) to the normalized contact maps. *homepage*: http://nservant.github.io/HiC-Pro ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.9.0`` ``-Python-2.7.12`` ``foss/2016b`` ========= ================== ============== .. _list_software_HiCExplorer_1093: *HiCExplorer* +++++++++++++ HiCexplorer addresses the common tasks of Hi-C analysis from processing to visualization. *homepage*: http://hicexplorer.readthedocs.org/ ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``2.1.1`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================= ============== .. _list_software_HIPS_308: *HIPS* ++++++ HIPS (Hierarchical Iterative Parallel Solver) is a scientific library that provides an efficient parallel iterative solver for very large sparse linear systems. *homepage*: http://hips.gforge.inria.fr/ ============ ============== version toolchain ============ ============== ``1.2b-rc5`` ``foss/2017b`` ============ ============== .. _list_software_HISAT2_427: *HISAT2* ++++++++ HISAT2 is a fast and sensitive alignment program for mapping next-generation sequencing reads (both DNA and RNA) against the general human population (as well as against a single reference genome). *homepage*: https://ccb.jhu.edu/software/hisat2/index.shtml ============== ================================================================================= version toolchain ============== ================================================================================= ``2.0.3-beta`` ``intel/2016a`` ``2.0.4`` ``foss/2016b`` ``2.0.5`` ``intel/2017a`` ``2.1.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ============== ================================================================================= .. _list_software_HLAminer_752: *HLAminer* ++++++++++ HLAminer is a software for HLA predictions from next-generation shotgun (NGS) sequence read data and supports direct read alignment and targeted de novo assembly of sequence reads. *homepage*: http://www.bcgsc.ca/platform/bioinfo/software/hlaminer ======= ================ ============== version versionsuffix toolchain ======= ================ ============== ``1.4`` ``-Perl-5.28.0`` ``foss/2018b`` ======= ================ ============== .. _list_software_HMMER_377: *HMMER* +++++++ HMMER is used for searching sequence databases for homologs of protein sequences, and for making protein sequence alignments. It implements methods using probabilistic models called profile hidden Markov models (profile HMMs). Compared to BLAST, FASTA, and other sequence alignment and database search tools based on older scoring methodology, HMMER aims to be significantly more accurate and more able to detect remote homologs because of the strength of its underlying mathematical models. In the past, this strength came at significant computational expense, but in the new HMMER3 project, HMMER is now essentially as fast as BLAST. *homepage*: http://hmmer.org/ ========= ============================================================================================================================================ version toolchain ========= ============================================================================================================================================ ``3.1b2`` ``GCC/6.4.0-2.28``, ``foss/2016a``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017a``, ``intel/2018a`` ``3.2.1`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``gompi/2019b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iimpi/2019b``, ``intel/2018b`` ========= ============================================================================================================================================ .. _list_software_hmmlearn_852: *hmmlearn* ++++++++++ hmmlearn is a set of algorithms for unsupervised learning and inference of Hidden Markov Models *homepage*: https://github.com/hmmlearn/hmmlearn ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.2.0`` ``-Python-2.7.14`` ``intel/2017b`` ========= ================== =============== .. _list_software_HOME_297: *HOME* ++++++ HOME (histogram of methylation) is a python package for differential methylation region (DMR) identification. The method uses histogram of methylation features and the linear Support Vector Machine (SVM) to identify DMRs from whole genome bisulfite sequencing (WGBS) data. *homepage*: https://github.com/ListerLab/HOME ======= ================== ============== version versionsuffix toolchain ======= ================== ============== ``0.9`` ``-Python-2.7.13`` ``foss/2017a`` ======= ================== ============== .. _list_software_Horovod_737: *Horovod* +++++++++ Horovod is a distributed training framework for TensorFlow. *homepage*: https://github.com/uber/horovod ========== =================================== ================== version versionsuffix toolchain ========== =================================== ================== ``0.9.10`` ``-Python-3.6.3`` ``intel/2017b`` ``0.18.1`` ``-Python-3.7.2`` ``foss/2019a`` ``0.18.2`` ``-TensorFlow-1.15.0-Python-3.7.4`` ``fosscuda/2019b`` ``0.18.2`` ``-TensorFlow-2.0.0-Python-3.7.4`` ``fosscuda/2019b`` ========== =================================== ================== .. _list_software_horton_666: *horton* ++++++++ HORTON is a Helpful Open-source Research TOol for N-fermion systems, written primarily in the Python programming language. (HORTON is named after the helpful pachyderm, not the Canadian caffeine supply store.) The ultimate goal of HORTON is to provide a platform for testing new ideas on the quantum many-body problem at a reasonable computational cost. Although HORTON is primarily designed to be a quantum-chemistry program, it can perform computations involving model Hamiltonians, and could be extended for computations in nuclear physics. *homepage*: https://theochem.github.io/horton ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``2.1.1`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ========= ================== =============================== .. _list_software_HPCG_290: *HPCG* ++++++ The HPCG Benchmark project is an effort to create a more relevant metric for ranking HPC systems than the High Performance LINPACK (HPL) benchmark, that is currently used by the TOP500 benchmark. *homepage*: https://software.sandia.gov/hpcg ======= =============================================== version toolchain ======= =============================================== ``3.0`` ``foss/2016b``, ``foss/2018b``, ``intel/2018b`` ``3.1`` ``foss/2018b``, ``intel/2018b`` ======= =============================================== .. _list_software_HPCX_307: *HPCX* ++++++ The Mellanox HPC-X Toolkit is a comprehensive MPI and SHMEM/PGAS software suite for high performance computing environments *homepage*: http://www.mellanox.com/page/products_dyn?product_family=189&mtag=hpc-x ========= ==================== version toolchain ========= ==================== ``2.3.0`` ``GCC/8.2.0-2.31.1`` ========= ==================== .. _list_software_HPDBSCAN_579: *HPDBSCAN* ++++++++++ Highly parallel density based spatial clustering for application with noise *homepage*: https://bitbucket.org/markus.goetz/hpdbscan ============ ============== version toolchain ============ ============== ``20171110`` ``foss/2017b`` ============ ============== .. _list_software_HPL_228: *HPL* +++++ HPL is a software package that solves a (random) dense linear system in double precision (64 bits) arithmetic on distributed-memory computers. It can thus be regarded as a portable as well as freely available implementation of the High Performance Computing Linpack Benchmark. *homepage*: http://www.netlib.org/benchmark/hpl/ ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= version toolchain ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= ``2.1`` ``foss/2016.04``, ``foss/2016.06``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gmpolf/2016a``, ``gmvolf/1.7.20``, ``gmvolf/2016a``, ``intel/2016.00``, ``intel/2016.01``, ``intel/2016.02-GCC-4.9``, ``intel/2016.02-GCC-5.3``, ``intel/2016.03-GCC-4.9``, ``intel/2016.03-GCC-5.3``, ``intel/2016.03-GCC-5.4``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``pomkl/2016.03``, ``pomkl/2016.04``, ``pomkl/2016.09`` ``2.2`` ``foss/2016.07``, ``foss/2016.09``, ``foss/2017a``, ``foss/2017b``, ``foss/2018.08``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2018b``, ``giolf/2017b``, ``giolf/2018a``, ``giolfc/2017b``, ``gmpolf/2017.10``, ``gomkl/2018b``, ``intel/2017.00``, ``intel/2017.01``, ``intel/2017.02``, ``intel/2017.09``, ``intel/2017a``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01``, ``intel/2018.02``, ``intel/2018.04``, ``intel/2018a``, ``intel/2018b``, ``intel/2019.00``, ``intel/2019.01``, ``intelcuda/2016.10``, ``intelcuda/2017b``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2016.09-GCC-5.4.0-2.26``, ``iomkl/2017.01``, ``iomkl/2017a``, ``iomkl/2017b``, ``iomkl/2018.02``, ``iomkl/2018a``, ``iomkl/2018b``, ``pomkl/2016.09`` ``2.3`` ``CrayCCE/19.06``, ``CrayGNU/19.06``, ``CrayIntel/19.06``, ``foss/2019a``, ``foss/2019b``, ``fosscuda/2019b``, ``gomkl/2019a``, ``intel/2019.02``, ``intel/2019.03``, ``intel/2019a``, ``intel/2019b``, ``intel/2020.00``, ``intelcuda/2019b``, ``iomkl/2019.01`` ======= ========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= .. _list_software_htop_443: *htop* ++++++ An interactive process viewer for Unix *homepage*: http://hisham.hm/htop/ ========= ========== version toolchain ========= ========== ``2.0.0`` ``system`` ``2.0.1`` ``system`` ========= ========== .. _list_software_HTSeq_453: *HTSeq* +++++++ A framework to process and analyze data from high-throughput sequencing (HTS) assays *homepage*: http://www-huber.embl.de/users/anders/HTSeq/ =========== ================== ================================================ version versionsuffix toolchain =========== ================== ================================================ ``0.6.1p1`` ``-Python-2.7.11`` ``foss/2016a`` ``0.6.1p1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``0.9.1`` ``-Python-2.7.12`` ``foss/2016b`` ``0.9.1`` ``-Python-2.7.13`` ``intel/2017a`` ``0.9.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``0.9.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``0.10.0`` ``-Python-2.7.14`` ``foss/2018a`` ``0.11.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``0.11.2`` ``-Python-3.6.6`` ``foss/2018b`` ``0.11.2`` ``-Python-3.7.2`` ``foss/2019a`` =========== ================== ================================================ .. _list_software_HTSlib_550: *HTSlib* ++++++++ PacBio fork of C library for reading/writing high-throughput sequencing data. This package includes the utilities bgzip and tabix *homepage*: https://github.com/PacificBiosciences/htslib ============ ============= =========================================================================================================================================================== version versionsuffix toolchain ============ ============= =========================================================================================================================================================== ``1.2.1`` ``foss/2016b`` ``1.3`` ``foss/2016a``, ``intel/2016a`` ``1.3.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``1.3.2`` ``intel/2016b`` ``1.4`` ``foss/2016b``, ``intel/2016b`` ``1.4.1`` ``foss/2016a``, ``intel/2017a`` ``1.6`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` ``1.7`` ``intel/2018a`` ``1.8`` ``foss/2018a``, ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``20160107`` ``-PacBio`` ``intel/2017a`` ============ ============= =========================================================================================================================================================== .. _list_software_hub_319: *hub* +++++ hub is a command-line wrapper for git that makes you better at GitHub. *homepage*: https://hub.github.com/ ========= ================ ========== version versionsuffix toolchain ========= ================ ========== ``2.2.2`` ``-linux-amd64`` ``system`` ========= ================ ========== .. _list_software_hunspell_875: *hunspell* ++++++++++ Hunspell is a spell checker and morphological analyzer library and program designed for languages with rich morphology and complex word compounding or character encoding. *homepage*: http://hunspell.github.io/ ========= ================= version toolchain ========= ================= ``1.6.1`` ``intel/2017a`` ``1.7.0`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_hwloc_541: *hwloc* +++++++ The Portable Hardware Locality (hwloc) software package provides a portable abstraction (across OS, versions, architectures, ...) of the hierarchical topology of modern architectures, including NUMA memory nodes, sockets, shared caches, cores and simultaneous multithreading. It also gathers various system attributes such as cache and memory information as well as the locality of I/O devices such as network interfaces, InfiniBand HCAs or GPUs. It primarily aims at helping applications with gathering information about modern computing hardware so as to exploit it accordingly and efficiently. *homepage*: https://www.open-mpi.org/projects/hwloc/ =========== ===================================================================================================================================================================================================================================================== version toolchain =========== ===================================================================================================================================================================================================================================================== ``1.7.2`` ``GCC/4.8.2`` ``1.8.1`` ``GCC/4.8.2``, ``GCC/4.8.3`` ``1.9`` ``GCC/4.8.3`` ``1.10.0`` ``GCC/4.9.2`` ``1.10.1`` ``GCC/4.8.4``, ``GNU/4.9.2-2.25`` ``1.11.0`` ``GNU/4.9.3-2.25`` ``1.11.1`` ``GCC/4.9.3`` ``1.11.2`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25`` ``1.11.3`` ``GCC/5.2.0``, ``GCC/5.3.0-2.26``, ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``PGI/16.3-GCC-4.9.3-2.25``, ``PGI/16.4-GCC-5.3.0-2.26``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` ``1.11.4`` ``GCC/6.2.0-2.27``, ``PGI/16.7-GCC-5.4.0-2.26``, ``iccifort/2017.1.132-GCC-5.4.0-2.26`` ``1.11.5`` ``GCC/5.4.0-2.26``, ``GCC/6.3.0-2.27``, ``iccifort/2017.1.132-GCC-6.3.0-2.27`` ``1.11.6`` ``GCC/6.3.0-2.28`` ``1.11.7`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0`` ``1.11.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``intel/2017a`` ``1.11.10`` ``GCCcore/7.3.0`` ``1.11.11`` ``GCCcore/8.2.0`` ``1.11.12`` ``GCCcore/8.3.0`` ``2.0.2`` ``GCCcore/8.2.0`` ``2.0.3`` ``GCCcore/8.3.0`` ``2.1.0`` ``GCCcore/9.2.0`` =========== ===================================================================================================================================================================================================================================================== .. _list_software_Hyperopt_859: *Hyperopt* ++++++++++ hyperopt is a Python library for optimizing over awkward search spaces with real-valued, discrete, and conditional dimensions. *homepage*: http://hyperopt.github.io/hyperopt/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.1`` ``-Python-2.7.14`` ``intel/2017b`` ``0.1.1`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================== =============== .. _list_software_hyperspy_900: *hyperspy* ++++++++++ HyperSpy is an open source Python library which provides tools to facilitate the interactive data analysis of multi-dimensional datasets that can be described as multi-dimensional arrays of a given signal (e.g. a 2D array of spectra a.k.a spectrum image) *homepage*: http://hyperspy.org/ ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``1.1.1`` ``-Python-3.5.2`` ``intel/2016b`` ========= ================= =============== .. _list_software_HyPhy_498: *HyPhy* +++++++ HyPhy (Hypothesis Testing using Phylogenies) is an open-source software package for the analysis of genetic sequences (in particular the inference of natural selection) using techniques in phylogenetics, molecular evolution, and machine learning *homepage*: https://veg.github.io/hyphy-site/ ========= =============== version toolchain ========= =============== ``2.5.1`` ``gompi/2019a`` ========= =============== .. _list_software_hypothesis_1104: *hypothesis* ++++++++++++ Hypothesis is an advanced testing library for Python. It lets you write tests which are parametrized by a source of examples, and then generates simple and comprehensible examples that make your tests fail. This lets you find more bugs in your code with less work. *homepage*: https://github.com/HypothesisWorks/hypothesis ========== ================= ================================== version versionsuffix toolchain ========== ================= ================================== ``4.5.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``4.23.4`` ``GCCcore/8.2.0`` ``4.44.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========== ================= ================================== .. _list_software_Hypre_520: *Hypre* +++++++ Hypre is a library for solving large, sparse linear systems of equations on massively parallel computers. The problems of interest arise in the simulation codes being developed at LLNL and elsewhere to study physical phenomena in the defense, environmental, energy, and biological sciences. *homepage*: https://computation.llnl.gov/projects/hypre-scalable-linear-solvers-multigrid-methods ========== =============================== version toolchain ========== =============================== ``2.11.1`` ``foss/2016a``, ``intel/2016a`` ``2.14.0`` ``foss/2018a``, ``intel/2018a`` ``2.15.1`` ``foss/2019a``, ``intel/2019a`` ========== =============================== .. _list_software_letter_i: *I* --- :ref:`list_software_i-cisTarget_1084` - :ref:`list_software_i-PI_303` - :ref:`list_software_I-TASSER_584` - :ref:`list_software_ICA-AROMA_618` - :ref:`list_software_icc_303` - :ref:`list_software_iccifort_851` - :ref:`list_software_iccifortcuda_1264` - :ref:`list_software_icmake_618` - :ref:`list_software_iCount_626` - :ref:`list_software_ICU_225` - :ref:`list_software_IDBA-UD_470` - :ref:`list_software_ieeg-cli_767` - :ref:`list_software_ifort_548` - :ref:`list_software_IGMPlot_636` - :ref:`list_software_igraph_635` - :ref:`list_software_IGV_230` - :ref:`list_software_IGVTools_759` - :ref:`list_software_iimpi_536` - :ref:`list_software_iimpic_635` - :ref:`list_software_IMa2_297` - :ref:`list_software_IMa2p_409` - :ref:`list_software_imageio_731` - :ref:`list_software_ImageJ_557` - :ref:`list_software_ImageMagick_1071` - :ref:`list_software_imake_519` - :ref:`list_software_IMB_216` - :ref:`list_software_imbalanced-learn_1599` - :ref:`list_software_imgaug_634` - :ref:`list_software_imkl_429` - :ref:`list_software_Imlib2_543` - :ref:`list_software_IMOD_297` - :ref:`list_software_impi_431` - :ref:`list_software_IMPUTE2_518` - :ref:`list_software_Inelastica_1021` - :ref:`list_software_Infernal_815` - :ref:`list_software_Infomap_714` - :ref:`list_software_inputproto_1124` - :ref:`list_software_Inspector_951` - :ref:`list_software_IntaRNA_621` - :ref:`list_software_INTEGRATE_675` - :ref:`list_software_INTEGRATE-Neo_1010` - :ref:`list_software_intel_540` - :ref:`list_software_IntelClusterChecker_1939` - :ref:`list_software_intelcuda_953` - :ref:`list_software_IntelPython_1150` - :ref:`list_software_InterProScan_1208` - :ref:`list_software_intltool_885` - :ref:`list_software_io_lib_622` - :ref:`list_software_iomkl_540` - :ref:`list_software_iompi_542` - :ref:`list_software_IOR_234` - :ref:`list_software_IOzone_596` - :ref:`list_software_Ipopt_524` - :ref:`list_software_ipp_329` - :ref:`list_software_IPy_274` - :ref:`list_software_ipyparallel_1183` - :ref:`list_software_ipyrad_649` - :ref:`list_software_IPython_715` - :ref:`list_software_IQ-TREE_503` - :ref:`list_software_IRkernel_796` - :ref:`list_software_IronPython_1050` - :ref:`list_software_ISL_232` - :ref:`list_software_ispc_431` - :ref:`list_software_itac_417` - :ref:`list_software_ITK_232` - :ref:`list_software_ITSTool_654` .. _list_software_i-cisTarget_1084: *i-cisTarget* +++++++++++++ An integrative genomics method for the prediction of regulatory features and cis-regulatory modules in Human, Mouse, and Fly *homepage*: https://gbiomed.kuleuven.be/apps/lcb/i-cisTarget ============ ================== =============== version versionsuffix toolchain ============ ================== =============== ``20160602`` ``-Python-2.7.11`` ``intel/2016a`` ============ ================== =============== .. _list_software_i-PI_303: *i-PI* ++++++ A Python wrapper for (ab initio) (path integrals) molecular dynamics *homepage*: https://github.com/i-pi/i-pi ================ ================== =============== version versionsuffix toolchain ================ ================== =============== ``1.0-20160213`` ``-Python-2.7.11`` ``intel/2016a`` ================ ================== =============== .. _list_software_I-TASSER_584: *I-TASSER* ++++++++++ I-TASSER is a set of pre-compiled binaries and scripts for protein structure and function modelling and comparison. *homepage*: http://zhanglab.ccmb.med.umich.edu/I-TASSER/ ======= ========== version toolchain ======= ========== ``4.0`` ``system`` ``4.2`` ``system`` ``5.1`` ``system`` ======= ========== .. _list_software_ICA-AROMA_618: *ICA-AROMA* +++++++++++ ICA-AROMA (i.e. 'ICA-based Automatic Removal Of Motion Artifacts') concerns a data-driven method to identify and remove motion-related independent components from fMRI data. *homepage*: https://github.com/maartenmennes/ICA-AROMA ============== ================= ============== version versionsuffix toolchain ============== ================= ============== ``0.4.4-beta`` ``-Python-3.6.6`` ``foss/2018b`` ============== ================= ============== .. _list_software_icc_303: *icc* +++++ C and C++ compiler from Intel *homepage*: http://software.intel.com/en-us/intel-compilers/ ============== ===================== ========== version versionsuffix toolchain ============== ===================== ========== ``2016.0.109`` ``system`` ``2016.0.109`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.1.150`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.2.181`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.2.181`` ``-GCC-5.3.0-2.26`` ``system`` ``2016.3.210`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.3.210`` ``-GCC-5.3.0-2.26`` ``system`` ``2016.3.210`` ``-GCC-5.4.0-2.26`` ``system`` ``2017.0.098`` ``-GCC-5.4.0-2.26`` ``system`` ``2017.1.132`` ``-GCC-5.4.0-2.26`` ``system`` ``2017.1.132`` ``-GCC-6.3.0-2.27`` ``system`` ``2017.2.174`` ``-GCC-6.3.0-2.27`` ``system`` ``2017.4.196`` ``-GCC-6.4.0-2.28`` ``system`` ``2017.5.239`` ``-GCC-6.4.0-2.28`` ``system`` ``2017.6.256`` ``-GCC-6.4.0-2.28`` ``system`` ``2017.7.259`` ``-GCC-6.4.0-2.28`` ``system`` ``2018.0.128`` ``-GCC-6.4.0-2.28`` ``system`` ``2018.1.163`` ``-GCC-6.4.0-2.28`` ``system`` ``2018.2.199`` ``-GCC-6.4.0-2.28`` ``system`` ``2018.3.222`` ``-GCC-7.3.0-2.30`` ``system`` ``2018.5.274`` ``-GCC-7.3.0-2.30`` ``system`` ``2019.0.117`` ``-GCC-8.2.0-2.31.1`` ``system`` ``2019.1.144`` ``-GCC-8.2.0-2.31.1`` ``system`` ``2019.2.187`` ``-GCC-8.2.0-2.31.1`` ``system`` ``2019.3.199`` ``-GCC-8.3.0-2.32`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ============== ===================== ========== .. _list_software_iccifort_851: *iccifort* ++++++++++ Intel C, C++ & Fortran compilers *homepage*: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ ============== ===================== ========== version versionsuffix toolchain ============== ===================== ========== ``2016.0.109`` ``system`` ``2016.0.109`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.1.150`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.2.181`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.2.181`` ``-GCC-5.3.0-2.26`` ``system`` ``2016.3.210`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.3.210`` ``-GCC-5.3.0-2.26`` ``system`` ``2016.3.210`` ``-GCC-5.4.0-2.26`` ``system`` ``2017.0.098`` ``-GCC-5.4.0-2.26`` ``system`` ``2017.1.132`` ``-GCC-5.4.0-2.26`` ``system`` ``2017.1.132`` ``-GCC-6.3.0-2.27`` ``system`` ``2017.2.174`` ``-GCC-6.3.0-2.27`` ``system`` ``2017.4.196`` ``-GCC-6.4.0-2.28`` ``system`` ``2017.5.239`` ``-GCC-6.4.0-2.28`` ``system`` ``2018.0.128`` ``-GCC-6.4.0-2.28`` ``system`` ``2018.1.163`` ``-GCC-6.4.0-2.28`` ``system`` ``2018.2.199`` ``-GCC-6.4.0-2.28`` ``system`` ``2018.3.222`` ``-GCC-7.3.0-2.30`` ``system`` ``2018.5.274`` ``-GCC-7.3.0-2.30`` ``system`` ``2019.0.117`` ``-GCC-8.2.0-2.31.1`` ``system`` ``2019.1.144`` ``-GCC-8.2.0-2.31.1`` ``system`` ``2019.2.187`` ``-GCC-8.2.0-2.31.1`` ``system`` ``2019.3.199`` ``-GCC-8.3.0-2.32`` ``system`` ``2019.4.243`` ``system`` ``2019.5.281`` ``system`` ``2020.0.166`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ============== ===================== ========== .. _list_software_iccifortcuda_1264: *iccifortcuda* ++++++++++++++ Intel C, C++ & Fortran compilers with CUDA toolkit *homepage*: (none) ============== =================== ========== version versionsuffix toolchain ============== =================== ========== ``2016.10`` ``system`` ``2017.4.196`` ``-GCC-6.4.0-2.28`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` ============== =================== ========== .. _list_software_icmake_618: *icmake* ++++++++ Icmake is a hybrid between a 'make' utility and a 'shell script' language. Originally, it was written to provide a useful tool for automatic program maintenance and system administrative tasks on old MS-DOS platforms. *homepage*: http://icmake.sourceforge.net/ =========== ============== version toolchain =========== ============== ``7.23.02`` ``foss/2016a`` =========== ============== .. _list_software_iCount_626: *iCount* ++++++++ iCount: protein-RNA interaction analysis is a Python module and associated command-line interface (CLI), which provides all the commands needed to process iCLIP data on protein-RNA interactions. *homepage*: https://github.com/tomazc/iCount ============ ================= ============== version versionsuffix toolchain ============ ================= ============== ``20180820`` ``-Python-3.6.6`` ``foss/2018b`` ============ ================= ============== .. _list_software_ICU_225: *ICU* +++++ ICU is a mature, widely used set of C/C++ and Java libraries providing Unicode and Globalization support for software applications. *homepage*: https://site.icu-project.org/home ======== ==================================== version toolchain ======== ==================================== ``61.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``64.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``65.1`` ``GCCcore/8.3.0`` ======== ==================================== .. _list_software_IDBA-UD_470: *IDBA-UD* +++++++++ IDBA-UD is a iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth. It is an extension of IDBA algorithm. IDBA-UD also iterates from small k to a large k. In each iteration, short and low-depth contigs are removed iteratively with cutoff threshold from low to high to reduce the errors in low-depth and high-depth regions. Paired-end reads are aligned to contigs and assembled locally to generate some missing k-mers in low-depth regions. With these technologies, IDBA-UD can iterate k value of de Bruijn graph to a very large value with less gaps and less branches to form long contigs in both low-depth and high-depth regions. *homepage*: http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/ ========= ==================================================== version toolchain ========= ==================================================== ``1.1.3`` ``GCC/8.2.0-2.31.1``, ``foss/2018a``, ``foss/2018b`` ========= ==================================================== .. _list_software_ieeg-cli_767: *ieeg-cli* ++++++++++ IEEG.ORG is a collaborative initiative funded by the National Institutes of Neurological Disorders and Stroke. This initiative seeks to advance research towards the understanding of epilepsy by providing a platform for sharing data, tools and expertise between researchers. *homepage*: https://www.ieeg.org/ =========== ========== version toolchain =========== ========== ``1.14.56`` ``system`` =========== ========== .. _list_software_ifort_548: *ifort* +++++++ Fortran compiler from Intel *homepage*: http://software.intel.com/en-us/intel-compilers/ ============== ===================== ========== version versionsuffix toolchain ============== ===================== ========== ``2016.0.109`` ``system`` ``2016.0.109`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.1.150`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.2.181`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.2.181`` ``-GCC-5.3.0-2.26`` ``system`` ``2016.3.210`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.3.210`` ``-GCC-5.3.0-2.26`` ``system`` ``2016.3.210`` ``-GCC-5.4.0-2.26`` ``system`` ``2017.0.098`` ``-GCC-5.4.0-2.26`` ``system`` ``2017.1.132`` ``-GCC-5.4.0-2.26`` ``system`` ``2017.1.132`` ``-GCC-6.3.0-2.27`` ``system`` ``2017.2.174`` ``-GCC-6.3.0-2.27`` ``system`` ``2017.4.196`` ``-GCC-6.4.0-2.28`` ``system`` ``2017.5.239`` ``-GCC-6.4.0-2.28`` ``system`` ``2017.6.256`` ``-GCC-6.4.0-2.28`` ``system`` ``2017.7.259`` ``-GCC-6.4.0-2.28`` ``system`` ``2018.0.128`` ``-GCC-6.4.0-2.28`` ``system`` ``2018.1.163`` ``-GCC-6.4.0-2.28`` ``system`` ``2018.2.199`` ``-GCC-6.4.0-2.28`` ``system`` ``2018.3.222`` ``-GCC-7.3.0-2.30`` ``system`` ``2018.5.274`` ``-GCC-7.3.0-2.30`` ``system`` ``2019.0.117`` ``-GCC-8.2.0-2.31.1`` ``system`` ``2019.1.144`` ``-GCC-8.2.0-2.31.1`` ``system`` ``2019.2.187`` ``-GCC-8.2.0-2.31.1`` ``system`` ``2019.3.199`` ``-GCC-8.3.0-2.32`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` ============== ===================== ========== .. _list_software_IGMPlot_636: *IGMPlot* +++++++++ IGMPlot is a free open-source program developed to identify molecular interactions and prepare data to build 2D and 3D representations of them in the molecular environment. *homepage*: http://igmplot.univ-reims.fr ========= ====================================== version toolchain ========= ====================================== ``2.4.2`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ========= ====================================== .. _list_software_igraph_635: *igraph* ++++++++ igraph is a collection of network analysis tools with the emphasis on efficiency, portability and ease of use. igraph is open source and free. igraph can be programmed in R, Python and C/C++. *homepage*: http://igraph.org ========= ================================================ version toolchain ========= ================================================ ``0.7.1`` ``foss/2018b``, ``intel/2016b``, ``intel/2017b`` ========= ================================================ .. _list_software_IGV_230: *IGV* +++++ This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. *homepage*: http://www.broadinstitute.org/software/igv/ ========== ================== ========== version versionsuffix toolchain ========== ================== ========== ``2.3.68`` ``-Java-1.7.0_80`` ``system`` ``2.3.80`` ``-Java-1.7.0_80`` ``system`` ``2.5.0`` ``-Java-11`` ``system`` ========== ================== ========== .. _list_software_IGVTools_759: *IGVTools* ++++++++++ This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files. See also http://www.broadinstitute.org/software/igv/igvtools_commandline. *homepage*: https://software.broadinstitute.org/software/igv/igvtools ========== ================== ========== version versionsuffix toolchain ========== ================== ========== ``2.3.68`` ``-Java-1.7.0_80`` ``system`` ``2.3.72`` ``-Java-1.7.0_80`` ``system`` ``2.3.75`` ``-Java-1.7.0_80`` ``system`` ``2.4.18`` ``-Java-1.8`` ``system`` ========== ================== ========== .. _list_software_iimpi_536: *iimpi* +++++++ Intel C/C++ and Fortran compilers, alongside Intel MPI. *homepage*: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ =========== ==================== ========== version versionsuffix toolchain =========== ==================== ========== ``8.1.5`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.00`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.01`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.02`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.02`` ``-GCC-5.3.0-2.26`` ``system`` ``2016.03`` ``-GCC-4.9.3-2.25`` ``system`` ``2016.03`` ``-GCC-5.3.0-2.26`` ``system`` ``2016.03`` ``-GCC-5.4.0-2.26`` ``system`` ``2016b`` ``system`` ``2017.00`` ``-GCC-5.4.0-2.26`` ``system`` ``2017.01`` ``-GCC-5.4.0-2.26`` ``system`` ``2017.02`` ``-GCC-6.3.0-2.27`` ``system`` ``2017.09`` ``system`` ``2017a`` ``system`` ``2017b`` ``system`` ``2018.00`` ``system`` ``2018.01`` ``system`` ``2018.02`` ``system`` ``2018.04`` ``system`` ``2018a`` ``system`` ``2018b`` ``system`` ``2019.00`` ``system`` ``2019.01`` ``system`` ``2019.02`` ``system`` ``2019.03`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` ``2020.00`` ``system`` ``system`` ``-GCC-system-2.29`` ``system`` =========== ==================== ========== .. _list_software_iimpic_635: *iimpic* ++++++++ Intel C/C++ and Fortran compilers, alongside Intel MPI and CUDA. *homepage*: (none) =========== ========== version toolchain =========== ========== ``2016.10`` ``system`` ``2017b`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` =========== ========== .. _list_software_IMa2_297: *IMa2* ++++++ IMa2 is a progam for population genetic analysis that can handle two or more populations. *homepage*: https://bio.cst.temple.edu/~hey/software/software.htm#IMa2 =========== ============== version toolchain =========== ============== ``8.27.12`` ``foss/2016a`` =========== ============== .. _list_software_IMa2p_409: *IMa2p* +++++++ IMa2p is a parallel implementation of IMa2, using OpenMPI-C++ - a Bayesian MCMC based method for inferring population demography under the IM (Isolation with Migration) model. http://dx.doi.org/10.1111/1755-0998.12437 *homepage*: https://github.com/arunsethuraman/ima2p ============ =============== version toolchain ============ =============== ``20151123`` ``foss/2016a`` ``20160804`` ``intel/2016b`` ============ =============== .. _list_software_imageio_731: *imageio* +++++++++ Imageio is a Python library that provides an easy interface to read and write a wide range of image data, including animated images, video, volumetric data, and scientific formats. *homepage*: https://imageio.github.io ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``2.3.0`` ``-Python-3.6.4`` ``intel/2018a`` ``2.5.0`` ``foss/2019a`` ========= ================= =============== .. _list_software_ImageJ_557: *ImageJ* ++++++++ Image Processing and Analysis in Java *homepage*: https://imagej.nih.gov/ij ========= ========== version toolchain ========= ========== ``1.51a`` ``system`` ``1.51i`` ``system`` ``1.51k`` ``system`` ========= ========== .. _list_software_ImageMagick_1071: *ImageMagick* +++++++++++++ ImageMagick is a software suite to create, edit, compose, or convert bitmap images *homepage*: https://www.imagemagick.org/ ============ =================================== =============================== version versionsuffix toolchain ============ =================================== =============================== ``6.9.4-8`` ``intel/2016a`` ``7.0.1-6`` ``intel/2016a`` ``7.0.1-9`` ``intel/2016a`` ``7.0.2-9`` ``intel/2016a`` ``7.0.3-1`` ``intel/2016b`` ``7.0.5-4`` ``intel/2017a`` ``7.0.5-10`` ``foss/2016b`` ``7.0.7-8`` ``-JasPer-1.900.1`` ``intel/2017a`` ``7.0.7-14`` ``foss/2017b``, ``intel/2017b`` ``7.0.7-15`` ``GCCcore/6.4.0`` ``7.0.7-26`` ``foss/2018a`` ``7.0.7-30`` ``GCCcore/6.4.0`` ``7.0.7-30`` ``-Ghostscript-9.22-cairo-1.14.12`` ``GCCcore/6.4.0`` ``7.0.7-39`` ``-Ghostscript-9.23-cairo-1.14.12`` ``GCCcore/6.4.0`` ``7.0.8-11`` ``GCCcore/7.3.0`` ``7.0.8-46`` ``GCCcore/8.2.0`` ``7.0.9-5`` ``GCCcore/8.3.0`` ============ =================================== =============================== .. _list_software_imake_519: *imake* +++++++ imake is a Makefile-generator that is intended to make it easier to develop software portably for multiple systems. *homepage*: http://www.x.org/ ========= =============== version toolchain ========= =============== ``1.0.7`` ``intel/2016a`` ========= =============== .. _list_software_IMB_216: *IMB* +++++ The Intel MPI Benchmarks perform a set of MPI performance measurements for point-to-point and global communication operations for a range of message sizes *homepage*: https://software.intel.com/en-us/articles/intel-mpi-benchmarks ========== ================================================================== version toolchain ========== ================================================================== ``4.1`` ``foss/2016a``, ``foss/2017a``, ``intel/2017.02``, ``intel/2017a`` ``2018.1`` ``intel/2017a`` ``2019.3`` ``gompi/2019a``, ``iimpi/2019a`` ========== ================================================================== .. _list_software_imbalanced-learn_1599: *imbalanced-learn* ++++++++++++++++++ imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance. *homepage*: https://github.com/scikit-learn-contrib/imbalanced-learn ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.2.1`` ``-Python-2.7.12`` ``intel/2016b`` ``0.2.1`` ``-Python-3.5.2`` ``intel/2016b`` ``0.3.3`` ``-Python-3.6.4`` ``foss/2018a`` ``0.4.3`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================== =============== .. _list_software_imgaug_634: *imgaug* ++++++++ This python library helps you with augmenting images for your machine learning projects. It converts a set of input images into a new, much larger set of slightly altered images. *homepage*: https://imgaug.readthedocs.io/en/latest/ ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``0.2.8`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== .. _list_software_imkl_429: *imkl* ++++++ Intel Math Kernel Library is a library of highly optimized, extensively threaded math routines for science, engineering, and financial applications that require maximum performance. Core math functions include BLAS, LAPACK, ScaLAPACK, Sparse Solvers, Fast Fourier Transforms, Vector Math, and more. *homepage*: https://software.intel.com/mkl ============== ====================================================================================================================================================================================================================================================================== version toolchain ============== ====================================================================================================================================================================================================================================================================== ``11.2.3.187`` ``gimpi/2.11.5`` ``11.3.0.109`` ``iimpi/2016.00-GCC-4.9.3-2.25`` ``11.3.1.150`` ``iimpi/2016.01-GCC-4.9.3-2.25``, ``iimpi/8.1.5-GCC-4.9.3-2.25`` ``11.3.2.181`` ``iimpi/2016.02-GCC-4.9.3-2.25``, ``iimpi/2016.02-GCC-5.3.0-2.26``, ``pompi/2016.03`` ``11.3.3.210`` ``iimpi/2016.03-GCC-4.9.3-2.25``, ``iimpi/2016.03-GCC-5.3.0-2.26``, ``iimpi/2016.03-GCC-5.4.0-2.26``, ``iimpi/2016b``, ``iimpic/2016.10``, ``iompi/2016.07``, ``iompi/2016.09-GCC-4.9.3-2.25``, ``iompi/2016.09-GCC-5.4.0-2.26``, ``pompi/2016.04``, ``pompi/2016.09`` ``2017.0.098`` ``iimpi/2017.00-GCC-5.4.0-2.26`` ``2017.1.132`` ``gimpi/2017a``, ``iimpi/2017.01-GCC-5.4.0-2.26``, ``iimpi/2017a``, ``iompi/2017.01``, ``iompi/2017a`` ``2017.2.174`` ``iimpi/2017.02-GCC-6.3.0-2.27`` ``2017.3.196`` ``gompi/2017b``, ``iimpi/2017b``, ``iimpic/2017b``, ``iompi/2017b`` ``2017.4.239`` ``iimpi/2017.09`` ``2018.0.128`` ``iimpi/2018.00`` ``2018.1.163`` ``iimpi/2018.01``, ``iimpi/2018a``, ``iompi/2018a`` ``2018.2.199`` ``iimpi/2018.02``, ``iompi/2018.02`` ``2018.3.222`` ``gimpi/2018b``, ``gompi/2018b``, ``iimpi/2018b``, ``iompi/2018b`` ``2018.4.274`` ``iimpi/2018.04`` ``2019.0.117`` ``iimpi/2019.00`` ``2019.1.144`` ``gompi/2019a``, ``iimpi/2019.01``, ``iimpi/2019a``, ``iimpic/2019a``, ``iompi/2019.01`` ``2019.2.187`` ``iimpi/2019.02`` ``2019.3.199`` ``iimpi/2019.03`` ``2019.5.281`` ``iimpi/2019b``, ``iimpic/2019b`` ``2020.0.166`` ``iimpi/2020.00`` ============== ====================================================================================================================================================================================================================================================================== .. _list_software_Imlib2_543: *Imlib2* ++++++++ This is the Imlib 2 library - a library that does image file loading and saving as well as rendering, manipulation, arbitrary polygon support, etc. It does ALL of these operations FAST. Imlib2 also tries to be highly intelligent about doing them, so writing naive programs can be done easily, without sacrificing speed. *homepage*: https://docs.enlightenment.org/api/imlib2/html/ ========= ================= version toolchain ========= ================= ``1.5.1`` ``GCCcore/6.4.0`` ========= ================= .. _list_software_IMOD_297: *IMOD* ++++++ IMOD is a set of image processing, modeling and display programs used for tomographic reconstruction and for 3D reconstruction of EM serial sections and optical sections. The package contains tools for assembling and aligning data within multiple types and sizes of image stacks, viewing 3-D data from any orientation, and modeling and display of the image files. IMOD was developed primarily by David Mastronarde, Rick Gaudette, Sue Held, Jim Kremer, Quanren Xiong, and John Heumann at the University of Colorado. *homepage*: http://bio3d.colorado.edu/imod/ ========== ===================== ========== version versionsuffix toolchain ========== ===================== ========== ``4.7.15`` ``_RHEL6-64_CUDA6.0`` ``system`` ========== ===================== ========== .. _list_software_impi_431: *impi* ++++++ The Intel(R) MPI Library for Linux* OS is a multi-fabric message passing library based on ANL MPICH2 and OSU MVAPICH2. The Intel MPI Library for Linux OS implements the Message Passing Interface, version 2 (MPI-2) specification. *homepage*: http://software.intel.com/en-us/intel-mpi-library/ ============== ============= ================================================================================================================================================================================================================================ version versionsuffix toolchain ============== ============= ================================================================================================================================================================================================================================ ``3.2.2.006`` ``system`` ``4.0.0.028`` ``system`` ``4.0.0.028`` ``-32bit`` ``system`` ``4.0.2.003`` ``system`` ``4.1.0.027`` ``system`` ``4.1.0.030`` ``system`` ``4.1.1.036`` ``system`` ``4.1.2.040`` ``system`` ``4.1.3.045`` ``system`` ``4.1.3.049`` ``GCC/4.8.3``, ``system`` ``5.0.3.048`` ``GCC/4.9.3`` ``5.1.1.109`` ``iccifort/2016.0.109-GCC-4.9.3-2.25`` ``5.1.2.150`` ``iccifort/2016.1.150-GCC-4.9.3-2.25`` ``5.1.3.181`` ``iccifort/2016.2.181-GCC-4.9.3-2.25``, ``iccifort/2016.2.181-GCC-5.3.0-2.26``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``iccifort/2016.3.210-GCC-5.3.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``iccifortcuda/2016.10`` ``2017.0.098`` ``iccifort/2017.0.098-GCC-5.4.0-2.26`` ``2017.1.132`` ``GCC/5.4.0-2.26``, ``iccifort/2017.1.132-GCC-5.4.0-2.26``, ``iccifort/2017.1.132-GCC-6.3.0-2.27`` ``2017.2.174`` ``iccifort/2017.2.174-GCC-6.3.0-2.27`` ``2017.3.196`` ``GCC/6.4.0-2.28``, ``gcccuda/2017b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifortcuda/2017.4.196-GCC-6.4.0-2.28`` ``2017.4.239`` ``iccifort/2017.5.239-GCC-6.4.0-2.28`` ``2018.0.128`` ``iccifort/2018.0.128-GCC-6.4.0-2.28`` ``2018.1.163`` ``GCC/6.4.0-2.28``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` ``2018.2.199`` ``iccifort/2018.2.199-GCC-6.4.0-2.28`` ``2018.3.222`` ``GCC/7.3.0-2.30``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` ``2018.4.274`` ``iccifort/2018.5.274-GCC-7.3.0-2.30``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``iccifortcuda/2019a`` ``2018.5.288`` ``iccifort/2019.5.281``, ``iccifortcuda/2019b`` ``2019.0.117`` ``iccifort/2019.0.117-GCC-8.2.0-2.31.1`` ``2019.1.144`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``2019.2.187`` ``iccifort/2019.2.187-GCC-8.2.0-2.31.1`` ``2019.3.199`` ``iccifort/2019.3.199-GCC-8.3.0-2.32`` ``2019.6.166`` ``iccifort/2020.0.166`` ``system`` ``iccifort/system-GCC-system-2.29`` ============== ============= ================================================================================================================================================================================================================================ .. _list_software_IMPUTE2_518: *IMPUTE2* +++++++++ IMPUTE version 2 (also known as IMPUTE2) is a genotype imputation and haplotype phasing program based on ideas from Howie et al. 2009 *homepage*: http://mathgen.stats.ox.ac.uk/impute/impute_v2.html ========= =================== ========== version versionsuffix toolchain ========= =================== ========== ``2.3.0`` ``_x86_64_dynamic`` ``system`` ``2.3.0`` ``_x86_64_static`` ``system`` ``2.3.2`` ``_x86_64_dynamic`` ``system`` ``2.3.2`` ``_x86_64_static`` ``system`` ========= =================== ========== .. _list_software_Inelastica_1021: *Inelastica* ++++++++++++ Python package for eigenchannels, vibrations and inelastic electron transport based on SIESTA/TranSIESTA DFT. *homepage*: https://github.com/tfrederiksen/inelastica ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.3.5`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============== .. _list_software_Infernal_815: *Infernal* ++++++++++ Infernal ("INFERence of RNA ALignment") is for searching DNA sequence databases for RNA structure and sequence similarities. *homepage*: http://eddylab.org/infernal/ ========= ================================================================ version toolchain ========= ================================================================ ``1.1.2`` ``foss/2016b``, ``foss/2018b``, ``intel/2017a``, ``intel/2018b`` ========= ================================================================ .. _list_software_Infomap_714: *Infomap* +++++++++ Multi-level network clustering based on the Map equation. *homepage*: https://www.mapequation.org/code.html#Linux ============ ==================== version toolchain ============ ==================== ``20190308`` ``GCC/8.2.0-2.31.1`` ============ ==================== .. _list_software_inputproto_1124: *inputproto* ++++++++++++ X.org InputProto protocol headers. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= version toolchain ========= ================================================= ``2.3.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``2.3.2`` ``intel/2016a`` ========= ================================================= .. _list_software_Inspector_951: *Inspector* +++++++++++ Intel Inspector XE is an easy to use memory error checker and thread checker for serial and parallel applications *homepage*: https://software.intel.com/en-us/intel-inspector-xe ================ ========== version toolchain ================ ========== ``2013_update6`` ``system`` ``2013_update7`` ``system`` ``2016_update3`` ``system`` ``2017_update1`` ``system`` ``2017_update2`` ``system`` ``2018_update1`` ``system`` ``2018_update2`` ``system`` ``2018_update3`` ``system`` ``2019_update2`` ``system`` ``2019_update5`` ``system`` ================ ========== .. _list_software_IntaRNA_621: *IntaRNA* +++++++++ Efficient RNA-RNA interaction prediction incorporating accessibility and seeding of interaction sites *homepage*: https://github.com/BackofenLab/IntaRNA ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.3.1`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== ============== .. _list_software_INTEGRATE_675: *INTEGRATE* +++++++++++ INTEGRATE is a tool calling gene fusions with exact fusion junctions and genomic breakpoints by combining RNA-Seq and WGS data. It is highly sensitive and accurate by applying a fast split-read mapping algorithm based on Burrow-Wheeler transform. *homepage*: https://sourceforge.net/p/integrate-fusion/wiki/Home/ ========= ================= version toolchain ========= ================= ``0.2.6`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_INTEGRATE-Neo_1010: *INTEGRATE-Neo* +++++++++++++++ INTEGRATE-Neo is a gene fusion neoantigen discovering tool using next-generation sequencing data. It is written in C++ and Python. *homepage*: ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``1.2.1`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== .. _list_software_intel_540: *intel* +++++++ Compiler toolchain including Intel compilers, Intel MPI and Intel Math Kernel Library (MKL). *homepage*: https://easybuild.readthedocs.io/en/master/Common-toolchains.html#intel-toolchain =========== ============= ========== version versionsuffix toolchain =========== ============= ========== ``2016.00`` ``system`` ``2016.01`` ``system`` ``2016.02`` ``-GCC-4.9`` ``system`` ``2016.02`` ``-GCC-5.3`` ``system`` ``2016.03`` ``-GCC-4.9`` ``system`` ``2016.03`` ``-GCC-5.3`` ``system`` ``2016.03`` ``-GCC-5.4`` ``system`` ``2016a`` ``system`` ``2016b`` ``system`` ``2017.00`` ``system`` ``2017.01`` ``system`` ``2017.02`` ``system`` ``2017.09`` ``system`` ``2017a`` ``system`` ``2017b`` ``system`` ``2018.00`` ``system`` ``2018.01`` ``system`` ``2018.02`` ``system`` ``2018.04`` ``system`` ``2018a`` ``system`` ``2018b`` ``system`` ``2019.00`` ``system`` ``2019.01`` ``system`` ``2019.02`` ``system`` ``2019.03`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` ``2020.00`` ``system`` =========== ============= ========== .. _list_software_IntelClusterChecker_1939: *IntelClusterChecker* +++++++++++++++++++++ Verifies cluster components work together ― for - better uptime and productivity and lower total - cost of ownership (TCO) *homepage*: https://software.intel.com/en-us/intel-cluster-checker ============== ========== version toolchain ============== ========== ``2017.1.016`` ``system`` ============== ========== .. _list_software_intelcuda_953: *intelcuda* +++++++++++ Intel Cluster Toolkit Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MPI & Intel MKL, with CUDA toolkit *homepage*: (none) =========== ========== version toolchain =========== ========== ``2016.10`` ``system`` ``2017b`` ``system`` ``2019a`` ``system`` ``2019b`` ``system`` =========== ========== .. _list_software_IntelPython_1150: *IntelPython* +++++++++++++ Intel® Distribution for Python. Powered by Anaconda. Accelerating Python* performance on modern architectures from Intel. *homepage*: https://software.intel.com/en-us/intel-distribution-for-python ========== =============== ========== version versionsuffix toolchain ========== =============== ========== ``2.7.15`` ``-2019.2.066`` ``system`` ``3.6.8`` ``-2019.2.066`` ``system`` ========== =============== ========== .. _list_software_InterProScan_1208: *InterProScan* ++++++++++++++ InterProScan is a sequence analysis application (nucleotide and protein sequences) that combines different protein signature recognition methods into one resource. *homepage*: http://www.ebi.ac.uk/interpro/ ============= =============== version toolchain ============= =============== ``5.26-65.0`` ``intel/2017b`` ``5.27-66.0`` ``intel/2017b`` ``5.28-67.0`` ``intel/2018a`` ============= =============== .. _list_software_intltool_885: *intltool* ++++++++++ intltool is a set of tools to centralize translation of many different file formats using GNU gettext-compatible PO files. *homepage*: http://freedesktop.org/wiki/Software/intltool/ ========== ================ ====================================================================================== version versionsuffix toolchain ========== ================ ====================================================================================== ``0.51.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``0.51.0`` ``-Perl-5.20.3`` ``intel/2016a`` ``0.51.0`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` ``0.51.0`` ``-Perl-5.24.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` ``0.51.0`` ``-Perl-5.24.1`` ``GCCcore/6.3.0``, ``intel/2017a`` ``0.51.0`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` ``0.51.0`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` ``0.51.0`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` ========== ================ ====================================================================================== .. _list_software_io_lib_622: *io_lib* ++++++++ Io_lib is a library of file reading and writing code to provide a general purpose trace file (and Experiment File) reading interface. The programmer simply calls the (eg) read_reading to create a "Read" C structure with the data loaded into memory. It has been compiled and tested on a variety of unix systems, MacOS X and MS Windows. *homepage*: http://sourceforge.net/projects/staden/files/io_lib/ ========== ============== version toolchain ========== ============== ``1.14.8`` ``foss/2016a`` ========== ============== .. _list_software_iomkl_540: *iomkl* +++++++ Intel Cluster Toolchain Compiler Edition provides Intel C/C++ and Fortran compilers, Intel MKL & OpenMPI. *homepage*: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ ========================== ========== version toolchain ========================== ========== ``2016.07`` ``system`` ``2016.09-GCC-4.9.3-2.25`` ``system`` ``2016.09-GCC-5.4.0-2.26`` ``system`` ``2017.01`` ``system`` ``2017a`` ``system`` ``2017b`` ``system`` ``2018.02`` ``system`` ``2018a`` ``system`` ``2018b`` ``system`` ``2019.01`` ``system`` ========================== ========== .. _list_software_iompi_542: *iompi* +++++++ Intel C/C++ and Fortran compilers, alongside Open MPI. *homepage*: http://software.intel.com/en-us/intel-cluster-toolkit-compiler/ ========================== ========== version toolchain ========================== ========== ``2016.07`` ``system`` ``2016.09-GCC-4.9.3-2.25`` ``system`` ``2016.09-GCC-5.4.0-2.26`` ``system`` ``2017.01`` ``system`` ``2017a`` ``system`` ``2017b`` ``system`` ``2018.02`` ``system`` ``2018a`` ``system`` ``2018b`` ``system`` ``2019.01`` ``system`` ========================== ========== .. _list_software_IOR_234: *IOR* +++++ The IOR software is used for benchmarking parallel file systems using POSIX, MPIIO, or HDF5 interfaces. *homepage*: https://github.com/IOR-LANL/ior ========= ============= =============== version versionsuffix toolchain ========= ============= =============== ``3.0.1`` ``-mpiio`` ``foss/2016a`` ``3.2.1`` ``gompi/2019b`` ========= ============= =============== .. _list_software_IOzone_596: *IOzone* ++++++++ IOzone is a filesystem benchmark tool. The benchmark generates and measures a variety of file operations. Iozone has been ported to many machines and runs under many operating systems. *homepage*: http://www.iozone.org/ ========= ============== version toolchain ========= ============== ``3.434`` ``foss/2016a`` ========= ============== .. _list_software_Ipopt_524: *Ipopt* +++++++ IPOPT (Interior Point Optimizer, pronounced Eye-Pea-Opt) is an open source software package for large-scale nonlinear optimization. *homepage*: https://projects.coin-or.org/Ipopt =========== =============== version toolchain =========== =============== ``3.12.9`` ``foss/2017b`` ``3.12.13`` ``intel/2019a`` =========== =============== .. _list_software_ipp_329: *ipp* +++++ Intel Integrated Performance Primitives (Intel IPP) is an extensive library of multicore-ready, highly optimized software functions for multimedia, data processing, and communications applications. Intel IPP offers thousands of optimized functions covering frequently used fundamental algorithms. *homepage*: https://software.intel.com/en-us/articles/intel-ipp/ ============== ========== version toolchain ============== ========== ``7.0.5.233`` ``system`` ``8.1.0.144`` ``system`` ``9.0.1.150`` ``system`` ``2017.1.132`` ``system`` ============== ========== .. _list_software_IPy_274: *IPy* +++++ Class and tools for handling of IPv4 and IPv6 addresses and networks *homepage*: https://pypi.python.org/pypi/IPy ======== ========== version toolchain ======== ========== ``0.83`` ``system`` ======== ========== .. _list_software_ipyparallel_1183: *ipyparallel* +++++++++++++ ipyparallel is a Python package and collection of CLI scripts for controlling clusters for Jupyter *homepage*: https://ipyparallel.readthedocs.io ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``6.2.2`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================= ============== .. _list_software_ipyrad_649: *ipyrad* ++++++++ ipyrad is an interactive toolkit for assembly and analysis of restriction-site associated genomic data sets (e.g., RAD, ddRAD, GBS) for population genetic and phylogenetic studies. *homepage*: https://ipyrad.readthedocs.io ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``0.6.15`` ``-Python-2.7.13`` ``intel/2017a`` ========== ================== =============== .. _list_software_IPython_715: *IPython* +++++++++ IPython provides a rich architecture for interactive computing with: Powerful interactive shells (terminal and Qt-based). A browser-based notebook with support for code, text, mathematical expressions, inline plots and other rich media. Support for interactive data visualization and use of GUI toolkits. Flexible, embeddable interpreters to load into your own projects. Easy to use, high performance tools for parallel computing. *homepage*: https://ipython.org/index.html ========= ================== ======================================================================================= version versionsuffix toolchain ========= ================== ======================================================================================= ``3.2.3`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``4.2.0`` ``-Python-2.7.11`` ``intel/2016a`` ``5.0.0`` ``-Python-2.7.11`` ``foss/2016a`` ``5.0.0`` ``-Python-3.5.1`` ``foss/2016a`` ``5.1.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``5.1.0`` ``-Python-3.5.2`` ``intel/2016b`` ``5.2.2`` ``-Python-2.7.12`` ``intel/2016b`` ``5.3.0`` ``-Python-2.7.13`` ``intel/2017a`` ``5.7.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``5.8.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``5.8.0`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``fosscuda/2018b``, ``fosscuda/2019a``, ``intel/2018b`` ``5.8.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``6.2.1`` ``-Python-3.6.4`` ``foss/2017a`` ``6.3.1`` ``-Python-3.6.4`` ``intel/2018a`` ``6.4.0`` ``-Python-3.6.4`` ``foss/2018a`` ``7.2.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``7.7.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``7.9.0`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== ======================================================================================= .. _list_software_IQ-TREE_503: *IQ-TREE* +++++++++ Efficient phylogenomic software by maximum likelihood *homepage*: http://www.iqtree.org/ ========= ============= =============== version versionsuffix toolchain ========= ============= =============== ``1.5.5`` ``-omp-mpi`` ``foss/2016a`` ``1.6.6`` ``intel/2018a`` ========= ============= =============== .. _list_software_IRkernel_796: *IRkernel* ++++++++++ The R kernel for the 'Jupyter' environment executes R code which the front-end (Jupyter Notebook or other front-ends) submits to the kernel via the network. *homepage*: https://irkernel.github.io ========== ========================== =============================== version versionsuffix toolchain ========== ========================== =============================== ``0.8.15`` ``-R-3.4.3-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ========== ========================== =============================== .. _list_software_IronPython_1050: *IronPython* ++++++++++++ IronPython is an open-source implementation of the Python programming language which is tightly integrated with the .NET Framework. IronPython can use the .NET Framework and Python libraries, and other .NET languages can use Python code just as easily. *homepage*: http://ironpython.net/ ======= =============== version toolchain ======= =============== ``2.7`` ``intel/2016b`` ======= =============== .. _list_software_ISL_232: *ISL* +++++ isl is a library for manipulating sets and relations of integer points bounded by linear constraints. *homepage*: http://isl.gforge.inria.fr/ ======== ====================================================== version toolchain ======== ====================================================== ``0.14`` ``GCC/4.9.2`` ``0.15`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a`` ``0.16`` ``GCC/4.9.3-2.25`` ``0.17`` ``foss/2016a`` ======== ====================================================== .. _list_software_ispc_431: *ispc* ++++++ Intel SPMD Program Compilers; An open-source compiler for high-performance SIMD programming on the CPU. ispc is a compiler for a variant of the C programming language, with extensions for 'single program, multiple data' (SPMD) programming. Under the SPMD model, the programmer writes a program that generally appears to be a regular serial program, though the execution model is actually that a number of program instances execute in parallel on the hardware. *homepage*: http://ispc.github.io/ , https://github.com/ispc/ispc/ ========== ========== version toolchain ========== ========== ``1.6.0`` ``system`` ``1.10.0`` ``system`` ========== ========== .. _list_software_itac_417: *itac* ++++++ The Intel Trace Collector is a low-overhead tracing library that performs event-based tracing in applications. The Intel Trace Analyzer provides a convenient way to monitor application activities gathered by the Intel Trace Collector through graphical displays. *homepage*: https://software.intel.com/en-us/intel-trace-analyzer/ ============== ========== version toolchain ============== ========== ``8.0.0.011`` ``system`` ``8.1.4.045`` ``system`` ``9.0.3.051`` ``system`` ``2017.1.024`` ``system`` ``2018.1.017`` ``system`` ``2018.3.022`` ``system`` ``2019.2.026`` ``system`` ============== ========== .. _list_software_ITK_232: *ITK* +++++ Insight Segmentation and Registration Toolkit (ITK) provides an extensive suite of software tools for registering and segmenting multidimensional imaging data. *homepage*: https://itk.org ========== ================== ============== version versionsuffix toolchain ========== ================== ============== ``4.12.2`` ``-Python-2.7.12`` ``foss/2016b`` ``4.13.0`` ``-Python-2.7.14`` ``foss/2018a`` ``4.13.0`` ``-Python-3.6.4`` ``foss/2018a`` ``4.13.1`` ``-Python-2.7.14`` ``foss/2018a`` ``4.13.1`` ``-Python-2.7.15`` ``foss/2018b`` ``4.13.1`` ``-Python-3.6.4`` ``foss/2018a`` ``4.13.1`` ``-Python-3.6.6`` ``foss/2018b`` ``5.0.1`` ``-Python-3.7.2`` ``foss/2019a`` ``5.0b01`` ``-Python-3.6.6`` ``foss/2018b`` ========== ================== ============== .. _list_software_ITSTool_654: *ITSTool* +++++++++ ITS Tool allows you to translate your XML documents with PO files *homepage*: http://itstool.org/ ========= ================== ================= version versionsuffix toolchain ========= ================== ================= ``2.0.5`` ``-Python-2.7.14`` ``intel/2018a`` ``2.0.5`` ``-Python-2.7.15`` ``foss/2018b`` ``2.0.6`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========= ================== ================= .. _list_software_letter_j: *J* --- :ref:`list_software_JAGS_293` - :ref:`list_software_Jansson_732` - :ref:`list_software_JasPer_581` - :ref:`list_software_Java_386` - :ref:`list_software_JAXFrontCE_884` - :ref:`list_software_jbigkit_740` - :ref:`list_software_Jellyfish_938` - :ref:`list_software_jemalloc_839` - :ref:`list_software_jhbuild_738` - :ref:`list_software_JiTCODE_546` - :ref:`list_software_jModelTest_1019` - :ref:`list_software_jq_219` - :ref:`list_software_JsonCpp_701` - :ref:`list_software_JUBE_294` - :ref:`list_software_Judy_412` - :ref:`list_software_Julia_501` - :ref:`list_software_JUnit_490` - :ref:`list_software_jupyterhub_1106` - :ref:`list_software_JWM_238` .. _list_software_JAGS_293: *JAGS* ++++++ JAGS is Just Another Gibbs Sampler. It is a program for analysis of Bayesian hierarchical models using Markov Chain Monte Carlo (MCMC) simulation *homepage*: http://mcmc-jags.sourceforge.net/ ========= ================================================ version toolchain ========= ================================================ ``4.2.0`` ``foss/2016a``, ``intel/2016a``, ``intel/2017a`` ``4.3.0`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b`` ========= ================================================ .. _list_software_Jansson_732: *Jansson* +++++++++ Jansson is a C library for encoding, decoding and manipulating JSON data. Its main features and design principles are: * Simple and intuitive API and data model * Comprehensive documentation * No dependencies on other libraries * Full Unicode support (UTF-8) * Extensive test suite *homepage*: http://www.digip.org/jansson/ ======= ============= version toolchain ======= ============= ``2.6`` ``GCC/4.8.3`` ======= ============= .. _list_software_JasPer_581: *JasPer* ++++++++ The JasPer Project is an open-source initiative to provide a free software-based reference implementation of the codec specified in the JPEG-2000 Part-1 standard. *homepage*: https://www.ece.uvic.ca/~frodo/jasper/ =========== ========================================================================================================================================================== version toolchain =========== ========================================================================================================================================================== ``1.900.1`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``2.0.10`` ``intel/2016b`` ``2.0.12`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` ``2.0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` =========== ========================================================================================================================================================== .. _list_software_Java_386: *Java* ++++++ Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers. *homepage*: http://java.com/ ======================= ========== version toolchain ======================= ========== ``1.6.0_24`` ``system`` ``1.7.0_10`` ``system`` ``1.7.0_15`` ``system`` ``1.7.0_21`` ``system`` ``1.7.0_40`` ``system`` ``1.7.0_45`` ``system`` ``1.7.0_60`` ``system`` ``1.7.0_75`` ``system`` ``1.7.0_76`` ``system`` ``1.7.0_79`` ``system`` ``1.7.0_80`` ``system`` ``1.8`` ``system`` ``1.8.0_20`` ``system`` ``1.8.0_25`` ``system`` ``1.8.0_31`` ``system`` ``1.8.0_40`` ``system`` ``1.8.0_45`` ``system`` ``1.8.0_60`` ``system`` ``1.8.0_65`` ``system`` ``1.8.0_66`` ``system`` ``1.8.0_72`` ``system`` ``1.8.0_74`` ``system`` ``1.8.0_77`` ``system`` ``1.8.0_92`` ``system`` ``1.8.0_112`` ``system`` ``1.8.0_121`` ``system`` ``1.8.0_131`` ``system`` ``1.8.0_141`` ``system`` ``1.8.0_144`` ``system`` ``1.8.0_152`` ``system`` ``1.8.0_162`` ``system`` ``1.8.0_172`` ``system`` ``1.8.0_181`` ``system`` ``1.8.0_192`` ``system`` ``1.8.0_202`` ``system`` ``1.8.0_212`` ``system`` ``1.8.0_221`` ``system`` ``1.8.0_231`` ``system`` ``1.8_191-b26-OpenJDK`` ``system`` ``1.9.0.4`` ``system`` ``11`` ``system`` ``11.0.2`` ``system`` ======================= ========== .. _list_software_JAXFrontCE_884: *JAXFrontCE* ++++++++++++ JAXFront is a technology to generate graphical user interfaces on multiple channels (Java Swing, HTML, PDF) on the basis of an XML schema. *homepage*: http://www.jaxfront.org/pages/free_community_edition.html ======== ========== version toolchain ======== ========== ``2.75`` ``system`` ======== ========== .. _list_software_jbigkit_740: *jbigkit* +++++++++ JBIG-KIT is a software implementation of the JBIG1 data compression standard (ITU-T T.82), which was designed for bi-level image data, such as scanned documents. *homepage*: ======= ==================================== version toolchain ======= ==================================== ``2.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ======= ==================================== .. _list_software_Jellyfish_938: *Jellyfish* +++++++++++ Jellyfish is a tool for fast, memory-efficient counting of k-mers in DNA. *homepage*: http://www.genome.umd.edu/jellyfish.html ========== =============================== version toolchain ========== =============================== ``1.1.11`` ``foss/2016a``, ``foss/2016b`` ``1.1.12`` ``foss/2018b``, ``intel/2018a`` ``2.2.6`` ``foss/2016b``, ``intel/2017a`` ``2.2.10`` ``foss/2018b``, ``intel/2018a`` ``2.3.0`` ``GCC/8.2.0-2.31.1`` ========== =============================== .. _list_software_jemalloc_839: *jemalloc* ++++++++++ jemalloc is a general purpose malloc(3) implementation that emphasizes fragmentation avoidance and scalable concurrency support. *homepage*: http://jemalloc.net ========= =============================== version toolchain ========= =============================== ``4.1.0`` ``intel/2016a`` ``4.2.0`` ``foss/2016a``, ``intel/2016a`` ``4.2.1`` ``intel/2016b`` ``4.5.0`` ``intel/2017a`` ``5.0.1`` ``GCCcore/6.4.0`` ``5.1.0`` ``GCCcore/7.3.0`` ``5.2.0`` ``GCCcore/8.2.0`` ``5.2.1`` ``GCCcore/8.3.0`` ========= =============================== .. _list_software_jhbuild_738: *jhbuild* +++++++++ JHBuild allows you to automatically download and compile “modules” (i.e. source code packages). Modules are listed in “module set” files, which also include dependency information so that JHBuild can discover what modules need to be built and in what order. *homepage*: https://wiki.gnome.org/action/show/Projects/Jhbuild =========== ================= version toolchain =========== ================= ``3.15.92`` ``GCCcore/4.9.3`` =========== ================= .. _list_software_JiTCODE_546: *JiTCODE* +++++++++ Just-in-time compilation for ordinary/delay/stochastic differential equations (DDEs) *homepage*: https://jitcde-common.readthedocs.io ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``1.3.2`` ``-Python-3.6.4`` ``intel/2018a`` ``1.4.0`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================= =============== .. _list_software_jModelTest_1019: *jModelTest* ++++++++++++ jModelTest is a tool to carry out statistical selection of best-fit models of nucleotide substitution. *homepage*: https://github.com/ddarriba/jmodeltest2 =================== ================== ========== version versionsuffix toolchain =================== ================== ========== ``2.1.10r20160303`` ``-Java-1.8.0_92`` ``system`` =================== ================== ========== .. _list_software_jq_219: *jq* ++++ jq is a lightweight and flexible command-line JSON processor. *homepage*: https://stedolan.github.io/jq/ ======= ================= version toolchain ======= ================= ``1.5`` ``GCCcore/6.4.0`` ======= ================= .. _list_software_JsonCpp_701: *JsonCpp* +++++++++ JsonCpp is a C++ library that allows manipulating JSON values, including serialization and deserialization to and from strings. It can also preserve existing comment in unserialization/serialization steps, making it a convenient format to store user input files. *homepage*: http://open-source-parsers.github.io/jsoncpp-docs/doxygen/index.html ========== ================= version toolchain ========== ================= ``0.10.7`` ``GCCcore/8.2.0`` ========== ================= .. _list_software_JUBE_294: *JUBE* ++++++ The JUBE benchmarking environment provides a script based framework to easily create benchmark sets, run those sets on different computer systems and evaluate the results. *homepage*: http://www.fz-juelich.de/jsc/jube ========= ========== version toolchain ========= ========== ``2.0.3`` ``system`` ``2.0.4`` ``system`` ``2.0.5`` ``system`` ========= ========== .. _list_software_Judy_412: *Judy* ++++++ A C library that implements a dynamic array. *homepage*: http://judy.sourceforge.net/ ========= ================= version toolchain ========= ================= ``1.0.5`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_Julia_501: *Julia* +++++++ Julia is a high-level, high-performance dynamic programming language for numerical computing *homepage*: https://julialang.org ========= ================= ========== version versionsuffix toolchain ========= ================= ========== ``1.1.1`` ``-linux-x86_64`` ``system`` ``1.2.0`` ``-linux-x86_64`` ``system`` ``1.3.1`` ``-linux-x86_64`` ``system`` ========= ================= ========== .. _list_software_JUnit_490: *JUnit* +++++++ A programmer-oriented testing framework for Java. *homepage*: http://sourceforge.net/projects/junit ======== =================== ========== version versionsuffix toolchain ======== =================== ========== ``4.10`` ``-Java-1.7.0_10`` ``system`` ``4.10`` ``-Java-1.7.0_21`` ``system`` ``4.11`` ``-Java-1.7.0_15`` ``system`` ``4.11`` ``-Java-1.7.0_21`` ``system`` ``4.11`` ``-Java-1.7.0_60`` ``system`` ``4.11`` ``-Java-1.7.0_75`` ``system`` ``4.11`` ``-Java-1.7.0_79`` ``system`` ``4.12`` ``-Java-1.7.0_80`` ``system`` ``4.12`` ``-Java-1.8`` ``system`` ``4.12`` ``-Java-1.8.0_112`` ``system`` ``4.12`` ``-Java-1.8.0_121`` ``system`` ``4.12`` ``-Java-1.8.0_144`` ``system`` ``4.12`` ``-Java-1.8.0_152`` ``system`` ``4.12`` ``-Java-1.8.0_162`` ``system`` ``4.12`` ``-Java-1.8.0_66`` ``system`` ``4.12`` ``-Java-1.8.0_72`` ``system`` ``4.12`` ``-Java-1.8.0_77`` ``system`` ``4.12`` ``-Java-1.8.0_92`` ``system`` ======== =================== ========== .. _list_software_jupyterhub_1106: *jupyterhub* ++++++++++++ JupyterHub is a multiuser version of the Jupyter (IPython) notebook designed for centralized deployments in companies, university classrooms and research labs. *homepage*: http://jupyter.org ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``0.6.1`` ``-Python-3.5.1`` ``foss/2016a`` ``0.8.1`` ``-Python-3.6.4`` ``foss/2017a`` ========= ================= ============== .. _list_software_JWM_238: *JWM* +++++ JWM is a light-weight window manager for the X11 Window System. *homepage*: https://joewing.net/projects/jwm/ ========= =============== version toolchain ========= =============== ``2.3.5`` ``intel/2016a`` ========= =============== .. _list_software_letter_k: *K* --- :ref:`list_software_Kaiju_500` - :ref:`list_software_kallisto_867` - :ref:`list_software_KAT_224` - :ref:`list_software_kbproto_769` - :ref:`list_software_Kent_tools_1058` - :ref:`list_software_Keras_502` - :ref:`list_software_khmer_535` - :ref:`list_software_kim-api_680` - :ref:`list_software_KMC_219` - :ref:`list_software_KmerGenie_887` - :ref:`list_software_KNIME_372` - :ref:`list_software_kpcalg_626` - :ref:`list_software_Kraken_604` - :ref:`list_software_Kraken2_654` - :ref:`list_software_Kratos_628` - :ref:`list_software_KronaTools_1036` - :ref:`list_software_kwant_549` - :ref:`list_software_KWIML_388` - :ref:`list_software_kWIP_347` - :ref:`list_software_KyotoCabinet_1228` .. _list_software_Kaiju_500: *Kaiju* +++++++ Kaiju is a program for sensitive taxonomic classification of high-throughput sequencing reads from metagenomic whole genome sequencing experiments *homepage*: http://kaiju.binf.ku.dk/ ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``1.5.0`` ``intel/2016b`` ``1.7.2`` ``-Python-3.7.2`` ``iimpi/2019a`` ========= ================= =============== .. _list_software_kallisto_867: *kallisto* ++++++++++ kallisto is a program for quantifying abundances of transcripts from RNA-Seq data, or more generally of target sequences using high-throughput sequencing reads. *homepage*: http://pachterlab.github.io/kallisto/ ========== ================================================ version toolchain ========== ================================================ ``0.42.5`` ``foss/2016a`` ``0.43.0`` ``intel/2016b`` ``0.43.1`` ``foss/2016b``, ``intel/2017a``, ``intel/2017b`` ``0.44.0`` ``foss/2016b``, ``intel/2018a`` ``0.45.0`` ``foss/2018b`` ``0.45.1`` ``foss/2019a`` ``0.46.0`` ``intel/2019a`` ========== ================================================ .. _list_software_KAT_224: *KAT* +++++ The K-mer Analysis Toolkit (KAT) contains a number of tools that analyse and compare K-mer spectra. *homepage*: https://www.earlham.ac.uk/kat-tools ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``2.4.2`` ``-Python-3.6.4`` ``foss/2018a`` ``2.4.2`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================= ============== .. _list_software_kbproto_769: *kbproto* +++++++++ X.org KBProto protocol headers. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================================== version toolchain ========= ================================================================== ``1.0.7`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017b`` ========= ================================================================== .. _list_software_Kent_tools_1058: *Kent_tools* ++++++++++++ Kent tools: collection of tools used by the UCSC genome browser. *homepage*: http://genome.cse.ucsc.edu/ ============ ================= ========== version versionsuffix toolchain ============ ================= ========== ``20130806`` ``-linux.x86_64`` ``system`` ``20171107`` ``-linux.x86_64`` ``system`` ``20180716`` ``-linux.x86_64`` ``system`` ``20190326`` ``-linux.x86_64`` ``system`` ============ ================= ========== .. _list_software_Keras_502: *Keras* +++++++ Keras is a minimalist, highly modular neural networks library, written in Python and capable of running on top of either TensorFlow or Theano. *homepage*: https://keras.io/ ========= ================== ================================== version versionsuffix toolchain ========= ================== ================================== ``1.0.8`` ``-Python-3.5.2`` ``intel/2016b`` ``1.1.0`` ``-Python-3.5.2`` ``intel/2016b`` ``2.0.4`` ``-Python-2.7.13`` ``intel/2017a`` ``2.0.4`` ``-Python-3.6.1`` ``intel/2017a`` ``2.0.5`` ``-Python-3.6.1`` ``intel/2017a`` ``2.0.8`` ``-Python-3.6.1`` ``intel/2017a`` ``2.1.1`` ``-Python-2.7.14`` ``intel/2017b`` ``2.1.1`` ``-Python-3.6.3`` ``intel/2017b`` ``2.1.2`` ``-Python-2.7.14`` ``intel/2017b`` ``2.1.2`` ``-Python-3.6.3`` ``foss/2017b`` ``2.1.3`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``2.2.0`` ``-Python-2.7.14`` ``fosscuda/2017b`` ``2.2.0`` ``-Python-3.6.3`` ``fosscuda/2017b`` ``2.2.0`` ``-Python-3.6.4`` ``foss/2018a`` ``2.2.2`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``2.2.4`` ``-Python-3.6.4`` ``intel/2018a`` ``2.2.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``2.2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ========= ================== ================================== .. _list_software_khmer_535: *khmer* +++++++ In-memory nucleotide sequence k-mer counting, filtering, graph traversal and more *homepage*: https://github.com/ged-lab/khmer/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.4.1`` ``-Python-2.7.12`` ``foss/2016b`` ``2.1.1`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== .. _list_software_kim-api_680: *kim-api* +++++++++ Open Knowledgebase of Interatomic Models. KIM is an API and OpenKIM is a collection of interatomic models (potentials) for atomistic simulations. This is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models can be installed with the package openkim-models, or the user can install them manually by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all. *homepage*: https://openkim.org/ ========= =============================== version toolchain ========= =============================== ``2.1.2`` ``foss/2019a``, ``intel/2019a`` ========= =============================== .. _list_software_KMC_219: *KMC* +++++ KMC is a disk-based programm for counting k-mers from (possibly gzipped) FASTQ/FASTA files. *homepage*: http://sun.aei.polsl.pl/kmc ========= ================= ============================== version versionsuffix toolchain ========= ================= ============================== ``3.1.0`` ``foss/2018a``, ``foss/2018b`` ``3.1.1`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` ========= ================= ============================== .. _list_software_KmerGenie_887: *KmerGenie* +++++++++++ KmerGenie estimates the best k-mer length for genome de novo assembly. *homepage*: http://kmergenie.bx.psu.edu/ ========== =============== version toolchain ========== =============== ``1.7044`` ``intel/2017a`` ``1.7048`` ``intel/2018a`` ========== =============== .. _list_software_KNIME_372: *KNIME* +++++++ KNIME Analytics Platform is the open source software for creating data science applications and services. KNIME stands for KoNstanz Information MinEr. *homepage*: https://www.knime.com/ ========= ========== version toolchain ========= ========== ``3.6.2`` ``system`` ========= ========== .. _list_software_kpcalg_626: *kpcalg* ++++++++ Kernel PC (kPC) algorithm for causal structure learning and causal inference using graphical models. kPC is a version of PC algorithm that uses kernel based independence criteria in order to be able to deal with non-linear relationships and non-Gaussian noise. Includes pcalg: Functions for causal structure learning and causal inference using graphical models. *homepage*: https://cran.r-project.org/package=kpcalg ========= ============= ============== version versionsuffix toolchain ========= ============= ============== ``1.0.1`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== .. _list_software_Kraken_604: *Kraken* ++++++++ Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. *homepage*: https://ccb.jhu.edu/software/kraken/ =============== ================ ================= version versionsuffix toolchain =============== ================ ================= ``0.10.5-beta`` ``-Perl-5.22.1`` ``foss/2016a`` ``0.10.5-beta`` ``-Perl-5.24.0`` ``foss/2016b`` ``1.0`` ``-Perl-5.26.1`` ``intel/2018a`` ``1.1`` ``-Perl-5.28.0`` ``foss/2018b`` ``1.1.1`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` =============== ================ ================= .. _list_software_Kraken2_654: *Kraken2* +++++++++ Kraken is a system for assigning taxonomic labels to short DNA sequences, usually obtained through metagenomic studies. Previous attempts by other bioinformatics software to accomplish this task have often used sequence alignment or machine learning techniques that were quite slow, leading to the development of less sensitive but much faster abundance estimation programs. Kraken aims to achieve high sensitivity and high speed by utilizing exact alignments of k-mers and a novel classification algorithm. *homepage*: http://www.ccb.jhu.edu/software/kraken2/ ============== ================ ============== version versionsuffix toolchain ============== ================ ============== ``2.0.6-beta`` ``-Perl-5.26.1`` ``foss/2018a`` ``2.0.7-beta`` ``-Perl-5.28.0`` ``foss/2018b`` ============== ================ ============== .. _list_software_Kratos_628: *Kratos* ++++++++ Kratos Multiphysics (A.K.A Kratos) is a framework for building parallel multi-disciplinary simulation software. *homepage*: http://www.cimne.com/kratos ======= ================= ============== version versionsuffix toolchain ======= ================= ============== ``6.0`` ``-Python-3.6.4`` ``foss/2018a`` ======= ================= ============== .. _list_software_KronaTools_1036: *KronaTools* ++++++++++++ Krona Tools is a set of scripts to create Krona charts from several Bioinformatics tools as well as from text and XML files. *homepage*: https://github.com/marbl/Krona/wiki/KronaTools ========= ================= version toolchain ========= ================= ``2.7`` ``GCCcore/7.3.0`` ``2.7.1`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_kwant_549: *kwant* +++++++ Kwant is a free (open source), powerful, and easy to use Python package for numerical calculations on tight-binding models with a strong focus on quantum transport. *homepage*: https://kwant-project.org/ ========= ================= =============================== version versionsuffix toolchain ========= ================= =============================== ``1.4.1`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ========= ================= =============================== .. _list_software_KWIML_388: *KWIML* +++++++ The Kitware Information Macro Library *homepage*: https://gitlab.kitware.com/utils/kwiml ============ ================= version toolchain ============ ================= ``20180201`` ``GCCcore/6.4.0`` ============ ================= .. _list_software_kWIP_347: *kWIP* ++++++ This software implements a de novo, alignment free measure of sample genetic dissimilarity which operates upon raw sequencing reads. It is able to calculate the genetic dissimilarity between samples without any reference genome, and without assembling one. *homepage*: https://github.com/kdmurray91/kWIP ========= ================= version toolchain ========= ================= ``0.2.0`` ``GCCcore/6.4.0`` ========= ================= .. _list_software_KyotoCabinet_1228: *KyotoCabinet* ++++++++++++++ Kyoto Cabinet is a library of routines for managing a database. *homepage*: https://fallabs.com/kyotocabinet ========== ================= version toolchain ========== ================= ``1.2.77`` ``GCCcore/7.3.0`` ========== ================= .. _list_software_letter_l: *L* --- :ref:`list_software_L_RNA_scaffolder_1540` - :ref:`list_software_LAME_287` - :ref:`list_software_LAST_308` - :ref:`list_software_LASTZ_398` - :ref:`list_software_lavaan_627` - :ref:`list_software_LCov_372` - :ref:`list_software_LeadIT_531` - :ref:`list_software_LEMON_379` - :ref:`list_software_Leptonica_927` - :ref:`list_software_less_439` - :ref:`list_software_LevelDB_638` - :ref:`list_software_lftp_438` - :ref:`list_software_libaio_624` - :ref:`list_software_libarchive_1049` - :ref:`list_software_libbitmask_1058` - :ref:`list_software_libcerf_727` - :ref:`list_software_libcircle_937` - :ref:`list_software_libcmaes_832` - :ref:`list_software_libconfig_941` - :ref:`list_software_libcpuset_971` - :ref:`list_software_libcroco_845` - :ref:`list_software_libctl_634` - :ref:`list_software_libdap_620` - :ref:`list_software_libdrm_634` - :ref:`list_software_libdwarf_843` - :ref:`list_software_libedit_733` - :ref:`list_software_libelf_622` - :ref:`list_software_libepoxy_876` - :ref:`list_software_libevent_857` - :ref:`list_software_libffcall_927` - :ref:`list_software_libffi_620` - :ref:`list_software_libFLAME_668` - :ref:`list_software_libfontenc_1060` - :ref:`list_software_libgcrypt_976` - :ref:`list_software_libgd_514` - :ref:`list_software_libgeotiff_1051` - :ref:`list_software_libglade_820` - :ref:`list_software_libGLU_543` - :ref:`list_software_libglvnd_850` - :ref:`list_software_libgpg-error_1228` - :ref:`list_software_libgpuarray_1186` - :ref:`list_software_libgtextutils_1428` - :ref:`list_software_libharu_743` - :ref:`list_software_libibmad_820` - :ref:`list_software_libibumad_937` - :ref:`list_software_libICE_520` - :ref:`list_software_libiconv_854` - :ref:`list_software_libidn_626` - :ref:`list_software_Libint_610` - :ref:`list_software_libjpeg-turbo_1334` - :ref:`list_software_libmatheval_1161` - :ref:`list_software_libmaus2_799` - :ref:`list_software_libMemcached_1198` - :ref:`list_software_libpciaccess_1253` - :ref:`list_software_libpng_636` - :ref:`list_software_libpsl_646` - :ref:`list_software_libpsml_755` - :ref:`list_software_libpsortb_977` - :ref:`list_software_libpthread-stubs_1661` - :ref:`list_software_libQGLViewer_1165` - :ref:`list_software_libreadline_1147` - :ref:`list_software_libRmath_819` - :ref:`list_software_librsvg_761` - :ref:`list_software_libsamplerate_1381` - :ref:`list_software_libsigc++_819` - :ref:`list_software_libsigsegv_1071` - :ref:`list_software_libSM_471` - :ref:`list_software_libsndfile_1052` - :ref:`list_software_libsodium_968` - :ref:`list_software_LibSoup_702` - :ref:`list_software_libspatialindex_1597` - :ref:`list_software_libspatialite_1383` - :ref:`list_software_libssh_645` - :ref:`list_software_LIBSVM_461` - :ref:`list_software_libtar_638` - :ref:`list_software_libtasn1_798` - :ref:`list_software_LibTIFF_576` - :ref:`list_software_libtirpc_857` - :ref:`list_software_libtool_757` - :ref:`list_software_libunistring_1306` - :ref:`list_software_libunwind_972` - :ref:`list_software_libutempter_1197` - :ref:`list_software_LibUUID_590` - :ref:`list_software_libvdwxc_867` - :ref:`list_software_libwebp_741` - :ref:`list_software_libX11_497` - :ref:`list_software_libXau_613` - :ref:`list_software_libxc_530` - :ref:`list_software_libxcb_628` - :ref:`list_software_libXcursor_1069` - :ref:`list_software_libXdamage_1006` - :ref:`list_software_libXdmcp_819` - :ref:`list_software_libXext_736` - :ref:`list_software_libXfixes_942` - :ref:`list_software_libXfont_838` - :ref:`list_software_libXft_617` - :ref:`list_software_libXi_504` - :ref:`list_software_libXinerama_1132` - :ref:`list_software_libxkbcommon_1285` - :ref:`list_software_libxml++_734` - :ref:`list_software_libxml2_698` - :ref:`list_software_libxml2-python_1417` - :ref:`list_software_libXmu_625` - :ref:`list_software_libXp_511` - :ref:`list_software_libXpm_620` - :ref:`list_software_libXrandr_934` - :ref:`list_software_libXrender_1039` - :ref:`list_software_libxslt_770` - :ref:`list_software_libxsmm_764` - :ref:`list_software_libXt_515` - :ref:`list_software_libXxf86vm_958` - :ref:`list_software_libyaml_746` - :ref:`list_software_libzip_650` - :ref:`list_software_lifelines_955` - :ref:`list_software_Lighter_719` - :ref:`list_software_likwid_644` - :ref:`list_software_LinBox_588` - :ref:`list_software_LittleCMS_849` - :ref:`list_software_LLVM_315` - :ref:`list_software_LMDB_287` - :ref:`list_software_LMfit_476` - :ref:`list_software_Lmod_396` - :ref:`list_software_LocARNA_576` - :ref:`list_software_LoFreq_585` - :ref:`list_software_Log-Log4perl_1112` - :ref:`list_software_LOHHLA_440` - :ref:`list_software_Loki_399` - :ref:`list_software_Longshot_846` - :ref:`list_software_lpsolve_773` - :ref:`list_software_lrslib_648` - :ref:`list_software_LS-PrePost_921` - :ref:`list_software_LSMS_319` - :ref:`list_software_Lua_290` - :ref:`list_software_LuaJIT_521` - :ref:`list_software_Lucene-Geo-Gazetteer_1916` - :ref:`list_software_LUMPY_407` - :ref:`list_software_LUSCUS_479` - :ref:`list_software_lwgrp_556` - :ref:`list_software_lxml_445` - :ref:`list_software_lynx_459` - :ref:`list_software_lz4_282` - :ref:`list_software_LZO_245` .. _list_software_L_RNA_scaffolder_1540: *L_RNA_scaffolder* ++++++++++++++++++ L_RNA_scaffolder is a novel scaffolding tool using long trancriptome reads to scaffold genome fragments *homepage*: http://www.fishbrowser.org/software/L_RNA_scaffolder/ ============ ================ =============== version versionsuffix toolchain ============ ================ =============== ``20141124`` ``-Perl-5.24.0`` ``intel/2016b`` ============ ================ =============== .. _list_software_LAME_287: *LAME* ++++++ LAME is a high quality MPEG Audio Layer III (MP3) encoder licensed under the LGPL. *homepage*: http://lame.sourceforge.net/ ========== =========================================================================================== version toolchain ========== =========================================================================================== ``3.99.5`` ``foss/2016b``, ``intel/2017a`` ``3.100`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b`` ========== =========================================================================================== .. _list_software_LAST_308: *LAST* ++++++ LAST finds similar regions between sequences. *homepage*: http://last.cbrc.jp/ ======= =============== version toolchain ======= =============== ``869`` ``intel/2017a`` ``914`` ``intel/2017b`` ======= =============== .. _list_software_LASTZ_398: *LASTZ* +++++++ LASTZ is a program for aligning DNA sequences, a pairwise aligner. Originally designed to handle sequences the size of human chromosomes and from different species, it is also useful for sequences produced by NGS sequencing technologies such as Roche 454. *homepage*: http://www.bx.psu.edu/~rsharris/lastz/ =========== ============== version toolchain =========== ============== ``1.02.00`` ``foss/2016a`` =========== ============== .. _list_software_lavaan_627: *lavaan* ++++++++ lavaan is a free, open source R package for latent variable analysis *homepage*: http://lavaan.org ============== ============= ============== version versionsuffix toolchain ============== ============= ============== ``0.6-4.1433`` ``-R-3.6.0`` ``foss/2019a`` ============== ============= ============== .. _list_software_LCov_372: *LCov* ++++++ LCOV - the LTP GCOV extension *homepage*: http://ltp.sourceforge.net/coverage/lcov.php ======== ================= version toolchain ======== ================= ``1.13`` ``GCCcore/7.2.0`` ======== ================= .. _list_software_LeadIT_531: *LeadIT* ++++++++ Visually Informed LeadOpt *homepage*: http://www.biosolveit.de/LeadIT/index.html ========= ========== version toolchain ========= ========== ``2.1.9`` ``system`` ========= ========== .. _list_software_LEMON_379: *LEMON* +++++++ LEMON stands for Library for Efficient Modeling and Optimization in Networks. It is a C++ template library providing efficient implementations of common data structures and algorithms with focus on combinatorial optimization tasks connected mainly with graphs and networks. *homepage*: https://lemon.cs.elte.hu ========= ==================== version toolchain ========= ==================== ``1.3.1`` ``GCC/8.2.0-2.31.1`` ========= ==================== .. _list_software_Leptonica_927: *Leptonica* +++++++++++ Leptonica is a collection of pedagogically-oriented open source software that is broadly useful for image processing and image analysis applications. *homepage*: http://www.leptonica.org ========== ================= version toolchain ========== ================= ``1.77.0`` ``GCCcore/7.3.0`` ``1.78.0`` ``GCCcore/8.2.0`` ========== ================= .. _list_software_less_439: *less* ++++++ Less is a free, open-source file pager. It can be found on most versions of Linux, Unix and Mac OS, as well as on many other operating systems. *homepage*: http://www.greenwoodsoftware.com/less/ ======= ============= version toolchain ======= ============= ``458`` ``GCC/4.8.2`` ======= ============= .. _list_software_LevelDB_638: *LevelDB* +++++++++ LevelDB is a fast key-value storage library written at Google that provides an ordered mapping from string keys to string values. *homepage*: https://github.com/google/leveldb ======== ================================================ version toolchain ======== ================================================ ``1.18`` ``foss/2016a``, ``intel/2017a``, ``intel/2017b`` ``1.20`` ``GCCcore/7.3.0`` ``1.22`` ``GCCcore/8.2.0`` ======== ================================================ .. _list_software_lftp_438: *lftp* ++++++ LFTP is a sophisticated ftp/http client, and a file transfer program supporting a number of network protocols. Like BASH, it has job control and uses the readline library for input. It has bookmarks, a built-in mirror command, and can transfer several files in parallel. It was designed with reliability in mind. *homepage*: http://lftp.yar.ru ========= ================== version toolchain ========= ================== ``4.6.4`` ``GNU/4.9.3-2.25`` ``4.8.4`` ``GCCcore/6.4.0`` ========= ================== .. _list_software_libaio_624: *libaio* ++++++++ Asynchronous input/output library that uses the kernels native interface. *homepage*: https://pagure.io/libaio =========== ================= version toolchain =========== ================= ``0.3.111`` ``GCCcore/8.2.0`` =========== ================= .. _list_software_libarchive_1049: *libarchive* ++++++++++++ Multi-format archive and compression library *homepage*: https://www.libarchive.org/ ========= ================= version toolchain ========= ================= ``3.4.0`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_libbitmask_1058: *libbitmask* ++++++++++++ libbitmask provides a convenient, powerful bitmask data type *homepage*: http://oss.sgi.com/projects/cpusets/ ======= ========== version toolchain ======= ========== ``2.0`` ``system`` ======= ========== .. _list_software_libcerf_727: *libcerf* +++++++++ libcerf is a self-contained numeric library that provides an efficient and accurate implementation of complex error functions, along with Dawson, Faddeeva, and Voigt functions. *homepage*: http://apps.jcns.fz-juelich.de/doku/sc/libcerf ======== ========================================================================================================= version toolchain ======== ========================================================================================================= ``1.4`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` ``1.5`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` ``1.7`` ``GCCcore/7.3.0`` ``1.11`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``1.13`` ``GCCcore/8.3.0`` ======== ========================================================================================================= .. _list_software_libcircle_937: *libcircle* +++++++++++ An API to provide an efficient distributed queue on a cluster. libcircle is an API for distributing embarrassingly parallel workloads using self-stabilization. *homepage*: https://github.com/hpc/libcircle/ ============== ================================ version toolchain ============== ================================ ``0.2.1-rc.1`` ``gompi/2019a``, ``iimpi/2019a`` ============== ================================ .. _list_software_libcmaes_832: *libcmaes* ++++++++++ libcmaes is a multithreaded C++11 library for high performance blackbox stochastic optimization using the CMA-ES algorithm for Covariance Matrix Adaptation Evolution Strategy. *homepage*: http://beniz.github.io/libcmaes/ ========= ============== version toolchain ========= ============== ``0.9.5`` ``foss/2016a`` ========= ============== .. _list_software_libconfig_941: *libconfig* +++++++++++ Libconfig is a simple library for processing structured configuration files *homepage*: https://hyperrealm.github.io/libconfig ========= ================= version toolchain ========= ================= ``1.5`` ``intel/2016b`` ``1.7.1`` ``GCCcore/6.4.0`` ``1.7.2`` ``GCCcore/7.3.0`` ========= ================= .. _list_software_libcpuset_971: *libcpuset* +++++++++++ libcpuset provides full access to cpuset capabilities *homepage*: http://oss.sgi.com/projects/cpusets/ ======= ========== version toolchain ======= ========== ``1.0`` ``system`` ======= ========== .. _list_software_libcroco_845: *libcroco* ++++++++++ Libcroco is a standalone css2 parsing and manipulation library. *homepage*: https://github.com/GNOME/libcroco ========== =============== version toolchain ========== =============== ``0.6.11`` ``intel/2016a`` ========== =============== .. _list_software_libctl_634: *libctl* ++++++++ libctl is a free Guile-based library implementing flexible control files for scientific simulations. *homepage*: http://ab-initio.mit.edu/libctl ========= ============== version toolchain ========= ============== ``3.2.2`` ``foss/2016a`` ========= ============== .. _list_software_libdap_620: *libdap* ++++++++ A C++ SDK which contains an implementation of DAP 2.0 and DAP4.0. This includes both Client- and Server-side support classes. *homepage*: https://www.opendap.org/software/libdap ========== ================== ================================================== version versionsuffix toolchain ========== ================== ================================================== ``3.18.1`` ``intel/2017a`` ``3.18.1`` ``-Python-2.7.11`` ``foss/2016a`` ``3.19.1`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b`` ``3.20.3`` ``GCCcore/7.3.0`` ``3.20.4`` ``GCCcore/8.2.0`` ========== ================== ================================================== .. _list_software_libdrm_634: *libdrm* ++++++++ Direct Rendering Manager runtime library. *homepage*: http://dri.freedesktop.org ========== ================================================== version toolchain ========== ================================================== ``2.4.67`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``2.4.68`` ``foss/2016a``, ``intel/2016a`` ``2.4.70`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` ``2.4.76`` ``GCCcore/6.3.0``, ``intel/2017a`` ``2.4.88`` ``GCCcore/6.4.0`` ``2.4.91`` ``GCCcore/6.4.0`` ``2.4.92`` ``GCCcore/7.3.0`` ``2.4.97`` ``GCCcore/8.2.0`` ``2.4.99`` ``GCCcore/8.3.0`` ========== ================================================== .. _list_software_libdwarf_843: *libdwarf* ++++++++++ The DWARF Debugging Information Format is of interest to programmers working on compilers and debuggers (and anyone interested in reading or writing DWARF information)) *homepage*: http://www.prevanders.net/dwarf.html ============ =================================================== version toolchain ============ =================================================== ``20140805`` ``GCC/4.9.2`` ``20150310`` ``GCC/4.9.2``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0`` ``20190529`` ``GCCcore/8.2.0`` ============ =================================================== .. _list_software_libedit_733: *libedit* +++++++++ This BSD-style licensed command line editor library provides generic line editing, history, and tokenization functions, similar to those found in GNU Readline. *homepage*: http://thrysoee.dk/editline/ ============ ================== version toolchain ============ ================== ``20150325`` ``GNU/4.9.3-2.25`` ``20180525`` ``GCCcore/6.4.0`` ============ ================== .. _list_software_libelf_622: *libelf* ++++++++ libelf is a free ELF object file access library *homepage*: http://www.mr511.de/software/english.html ========== ===================================================================================== version toolchain ========== ===================================================================================== ``0.8.13`` ``GCC/4.8.3``, ``GCC/4.9.2``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/8.2.0`` ========== ===================================================================================== .. _list_software_libepoxy_876: *libepoxy* ++++++++++ Epoxy is a library for handling OpenGL function pointer management for you *homepage*: https://github.com/anholt/libepoxy ========= ===================================== version toolchain ========= ===================================== ``1.5.3`` ``GCCcore/8.2.0``, ``fosscuda/2018b`` ========= ===================================== .. _list_software_libevent_857: *libevent* ++++++++++ The libevent API provides a mechanism to execute a callback function when a specific event occurs on a file descriptor or after a timeout has been reached. Furthermore, libevent also support callbacks due to signals or regular timeouts. *homepage*: http://libevent.org/ ========== ======================================================================== version toolchain ========== ======================================================================== ``2.0.22`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GNU/4.9.3-2.25`` ``2.1.8`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``system`` ``2.1.11`` ``GCCcore/8.3.0`` ========== ======================================================================== .. _list_software_libffcall_927: *libffcall* +++++++++++ GNU Libffcall is a collection of four libraries which can be used to build foreign function call interfaces in embedded interpreters *homepage*: https://www.gnu.org/software/libffcall/ ======== ================= version toolchain ======== ================= ``1.13`` ``GCCcore/6.4.0`` ======== ================= .. _list_software_libffi_620: *libffi* ++++++++ The libffi library provides a portable, high level programming interface to various calling conventions. This allows a programmer to call any function specified by a call interface description at run-time. *homepage*: http://sourceware.org/libffi/ ========= ============================================================================================================================================================================================================================================================================================================= version toolchain ========= ============================================================================================================================================================================================================================================================================================================= ``3.2.1`` ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``system`` ========= ============================================================================================================================================================================================================================================================================================================= .. _list_software_libFLAME_668: *libFLAME* ++++++++++ AMD fork of libFLAME. libFLAME is a portable library for dense matrix computations, providing much of the functionality present in LAPACK. *homepage*: https://developer.amd.com/amd-cpu-libraries/blas-library/#libflame ======= ============= ================== version versionsuffix toolchain ======= ============= ================== ``1.0`` ``-amd`` ``GCC/7.3.0-2.30`` ======= ============= ================== .. _list_software_libfontenc_1060: *libfontenc* ++++++++++++ X11 font encoding library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs/ ========= ================================================= version toolchain ========= ================================================= ``1.1.3`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= .. _list_software_libgcrypt_976: *libgcrypt* +++++++++++ Libgpg-error is a small library that defines common error values for all GnuPG components. *homepage*: https://gnupg.org/related_software/libgcrypt/index.html ========= ==================================== version toolchain ========= ==================================== ``1.6.5`` ``intel/2016a`` ``1.8.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ========= ==================================== .. _list_software_libgd_514: *libgd* +++++++ GD is an open source code library for the dynamic creation of images by programmers. *homepage*: https://libgd.github.io/ ========= ============================================================================================================ version toolchain ========= ============================================================================================================ ``2.1.1`` ``foss/2016a``, ``intel/2016a`` ``2.2.3`` ``foss/2016b``, ``intel/2016b`` ``2.2.4`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2017a`` ``2.2.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017b``, ``intel/2018a`` ========= ============================================================================================================ .. _list_software_libgeotiff_1051: *libgeotiff* ++++++++++++ Library for reading and writing coordinate system information from/to GeoTIFF files *homepage*: https://directory.fsf.org/wiki/Libgeotiff ========= =============================================== version toolchain ========= =============================================== ``1.4.2`` ``foss/2018a``, ``foss/2018b``, ``intel/2018b`` ``1.5.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= =============================================== .. _list_software_libglade_820: *libglade* ++++++++++ Libglade is a library for constructing user interfaces dynamically from XML descriptions. *homepage*: https://developer.gnome.org/libglade/ ========= ================================================================= version toolchain ========= ================================================================= ``2.6.4`` ``foss/2018b``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a`` ========= ================================================================= .. _list_software_libGLU_543: *libGLU* ++++++++ The OpenGL Utility Library (GLU) is a computer graphics library for OpenGL. *homepage*: ftp://ftp.freedesktop.org/pub/mesa/glu/ ========= ================ =========================================================================================================================================================================================================================================================================================================================================== version versionsuffix toolchain ========= ================ =========================================================================================================================================================================================================================================================================================================================================== ``9.0.0`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``fosscuda/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b``, ``iomkl/2018a`` ``9.0.0`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` ``9.0.1`` ``GCCcore/8.3.0`` ========= ================ =========================================================================================================================================================================================================================================================================================================================================== .. _list_software_libglvnd_850: *libglvnd* ++++++++++ libglvnd is a vendor-neutral dispatch layer for arbitrating OpenGL API calls between multiple vendors. *homepage*: https://github.com/NVIDIA/libglvnd ========= ==================================== version toolchain ========= ==================================== ``1.2.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ==================================== .. _list_software_libgpg-error_1228: *libgpg-error* ++++++++++++++ Libgpg-error is a small library that defines common error values for all GnuPG components. *homepage*: https://gnupg.org/related_software/libgpg-error/index.html ======== ================= version toolchain ======== ================= ``1.21`` ``intel/2016a`` ``1.35`` ``GCCcore/7.3.0`` ``1.36`` ``GCCcore/8.2.0`` ======== ================= .. _list_software_libgpuarray_1186: *libgpuarray* +++++++++++++ Library to manipulate tensors on the GPU. *homepage*: http://deeplearning.net/software/libgpuarray/ ========= ================== ======================================================== version versionsuffix toolchain ========= ================== ======================================================== ``0.7.5`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` ``0.7.5`` ``-Python-3.6.3`` ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``0.7.6`` ``fosscuda/2019a`` ``0.7.6`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``0.7.6`` ``-Python-3.6.6`` ``fosscuda/2018b`` ========= ================== ======================================================== .. _list_software_libgtextutils_1428: *libgtextutils* +++++++++++++++ ligtextutils is a dependency of fastx-toolkit and is provided via the same upstream *homepage*: http://hannonlab.cshl.edu/fastx_toolkit/ ======= ================================================================== version toolchain ======= ================================================================== ``0.7`` ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2018a`` ======= ================================================================== .. _list_software_libharu_743: *libharu* +++++++++ libHaru is a free, cross platform, open source library for generating PDF files. *homepage*: http://libharu.org/ ========= ====================================================================================================== version toolchain ========= ====================================================================================================== ``2.3.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2017a``, ``intel/2018b`` ========= ====================================================================================================== .. _list_software_libibmad_820: *libibmad* ++++++++++ libibmad is a convenience library to encode, decode, and dump IB MAD packets. It is implemented on top of and in conjunction with libibumad (the umad kernel interface library.) *homepage*: http://www.openfabrics.org ========== ================== version toolchain ========== ================== ``1.3.12`` ``GCC/4.9.3-2.25`` ========== ================== .. _list_software_libibumad_937: *libibumad* +++++++++++ libibumad is the umad kernel interface library. *homepage*: http://www.openfabrics.org ============ ================== version toolchain ============ ================== ``1.3.10.2`` ``GCC/4.9.3-2.25`` ============ ================== .. _list_software_libICE_520: *libICE* ++++++++ X Inter-Client Exchange library for freedesktop.org *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= version toolchain ========= ================================================= ``1.0.9`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= .. _list_software_libiconv_854: *libiconv* ++++++++++ Libiconv converts from one character encoding to another through Unicode conversion *homepage*: https://www.gnu.org/software/libiconv ======== ======================================================= version toolchain ======== ======================================================= ``1.15`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.16`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ======== ======================================================= .. _list_software_libidn_626: *libidn* ++++++++ GNU Libidn is a fully documented implementation of the Stringprep, Punycode and IDNA specifications. Libidn's purpose is to encode and decode internationalized domain names. *homepage*: http://www.gnu.org/software/libidn ======== ====================================================================================== version toolchain ======== ====================================================================================== ``1.32`` ``GCCcore/5.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` ``1.34`` ``GCCcore/6.4.0`` ``1.35`` ``GCCcore/7.3.0`` ======== ====================================================================================== .. _list_software_Libint_610: *Libint* ++++++++ Libint library is used to evaluate the traditional (electron repulsion) and certain novel two-body matrix elements (integrals) over Cartesian Gaussian functions used in modern atomic and molecular theory. *homepage*: https://github.com/evaleev/libint ========= ================================================================================================================================================================== version toolchain ========= ================================================================================================================================================================== ``1.1.4`` ``intel/2016a`` ``1.1.6`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2018a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ``2.0.3`` ``foss/2018b``, ``gompi/2019a``, ``intel/2018b`` ``2.1.0`` ``intel/2016b`` ``2.4.2`` ``intel/2018a`` ``2.5.0`` ``gompi/2019a``, ``iimpi/2019a`` ========= ================================================================================================================================================================== .. _list_software_libjpeg-turbo_1334: *libjpeg-turbo* +++++++++++++++ libjpeg-turbo is a fork of the original IJG libjpeg which uses SIMD to accelerate baseline JPEG compression and decompression. libjpeg is a library that implements JPEG image encoding, decoding and transcoding. *homepage*: https://sourceforge.net/projects/libjpeg-turbo/ ========= ================= ================================================================== version versionsuffix toolchain ========= ================= ================================================================== ``1.4.2`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` ``1.4.2`` ``-NASM-2.12.01`` ``foss/2016a``, ``intel/2016a`` ``1.5.0`` ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``1.5.1`` ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` ``1.5.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.5.3`` ``GCCcore/6.4.0`` ``2.0.0`` ``GCCcore/7.3.0`` ``2.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.0.3`` ``GCCcore/8.3.0`` ========= ================= ================================================================== .. _list_software_libmatheval_1161: *libmatheval* +++++++++++++ GNU libmatheval is a library (callable from C and Fortran) to parse and evaluate symbolic expressions input as text. *homepage*: http://www.gnu.org/software/libmatheval/ ========== ============================================================================================================================================ version toolchain ========== ============================================================================================================================================ ``1.1.11`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b`` ========== ============================================================================================================================================ .. _list_software_libmaus2_799: *libmaus2* ++++++++++ libmaus2 is a collection of data structures and algorithms. *homepage*: https://github.com/gt1/libmaus2 =========== =============== version toolchain =========== =============== ``2.0.453`` ``intel/2018a`` =========== =============== .. _list_software_libMemcached_1198: *libMemcached* ++++++++++++++ libMemcached is an open source C/C++ client library and tools for the memcached server (http://danga.com/memcached). It has been designed to be light on memory usage, thread safe, and provide full access to server side methods. *homepage*: https://memcached.org ========== ================= version toolchain ========== ================= ``1.0.18`` ``GCCcore/6.4.0`` ========== ================= .. _list_software_libpciaccess_1253: *libpciaccess* ++++++++++++++ Generic PCI access library. *homepage*: https://cgit.freedesktop.org/xorg/lib/libpciaccess/ ========== ============================================================================================= version toolchain ========== ============================================================================================= ``0.13.4`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``0.14`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``0.16`` ``GCCcore/9.2.0`` ========== ============================================================================================= .. _list_software_libpng_636: *libpng* ++++++++ libpng is the official PNG reference library *homepage*: http://www.libpng.org/pub/png/libpng.html ========== ===================================================================== version toolchain ========== ===================================================================== ``1.2.58`` ``system`` ``1.6.21`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``1.6.23`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``1.6.24`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` ``1.6.26`` ``foss/2016b``, ``intel/2016b`` ``1.6.27`` ``intel/2016b`` ``1.6.28`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``gimkl/2017a`` ``1.6.29`` ``GCCcore/6.3.0`` ``1.6.32`` ``GCCcore/6.4.0`` ``1.6.34`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.6.36`` ``GCCcore/8.2.0`` ``1.6.37`` ``GCCcore/8.3.0`` ========== ===================================================================== .. _list_software_libpsl_646: *libpsl* ++++++++ C library for the Public Suffix List *homepage*: https://rockdaboot.github.io/libpsl ========== ================= version toolchain ========== ================= ``0.20.2`` ``GCCcore/7.3.0`` ``0.21.0`` ``GCCcore/8.2.0`` ========== ================= .. _list_software_libpsml_755: *libpsml* +++++++++ LibPSML provides a Fortran API to parse files in the PSeudopotential Markup Language (PSML) format. *homepage*: https://launchpad.net/libpsml ========= ============================== version toolchain ========= ============================== ``1.1.7`` ``foss/2016b``, ``foss/2017a`` ========= ============================== .. _list_software_libpsortb_977: *libpsortb* +++++++++++ PSORT family of programs for subcellular localization prediction as well as other datasets and resources relevant to localization prediction. *homepage*: http://psort.org/ ======= ============== version toolchain ======= ============== ``1.0`` ``foss/2016a`` ======= ============== .. _list_software_libpthread-stubs_1661: *libpthread-stubs* ++++++++++++++++++ The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. *homepage*: http://xcb.freedesktop.org/ ======= ===================================================================================================== version toolchain ======= ===================================================================================================== ``0.3`` ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``0.4`` ``GCCcore/6.4.0`` ======= ===================================================================================================== .. _list_software_libQGLViewer_1165: *libQGLViewer* ++++++++++++++ libQGLViewer is a C++ library based on Qt that eases the creation of OpenGL 3D viewers. *homepage*: http://libqglviewer.com/ ========= ================ =============================================== version versionsuffix toolchain ========= ================ =============================================== ``2.6.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``2.6.3`` ``-Mesa-11.2.1`` ``foss/2016a``, ``intel/2016a`` ``2.6.4`` ``intel/2016b`` ``2.7.1`` ``intel/2018a`` ========= ================ =============================================== .. _list_software_libreadline_1147: *libreadline* +++++++++++++ The GNU Readline library provides a set of functions for use by applications that allow users to edit command lines as they are typed in. Both Emacs and vi editing modes are available. The Readline library includes additional functions to maintain a list of previously-entered command lines, to recall and perhaps reedit those lines, and perform csh-like history expansion on previous commands. *homepage*: http://cnswww.cns.cwru.edu/php/chet/readline/rltop.html ======= =================================================================================================================================================================================================================================================================================================================================================================================== version toolchain ======= =================================================================================================================================================================================================================================================================================================================================================================================== ``6.3`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``7.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``8.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` ======= =================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_libRmath_819: *libRmath* ++++++++++ The routines supporting the distribution and special functions in R and a few others are declared in C header file Rmath.h. These can be compiled into a standalone library for linking to other applications. *homepage*: https://cran.r-project.org/doc/manuals/r-release/R-admin.html#The-standalone-Rmath-library ========= ============== version toolchain ========= ============== ``3.6.0`` ``foss/2018b`` ========= ============== .. _list_software_librsvg_761: *librsvg* +++++++++ librsvg is a library to render SVG files using cairo. *homepage*: https://wiki.gnome.org/action/show/Projects/LibRsvg =========== =============== version toolchain =========== =============== ``2.40.15`` ``intel/2016a`` =========== =============== .. _list_software_libsamplerate_1381: *libsamplerate* +++++++++++++++ Secret Rabbit Code (aka libsamplerate) is a Sample Rate Converter for audio. *homepage*: http://www.mega-nerd.com/libsamplerate ========= ================= version toolchain ========= ================= ``0.1.9`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_libsigc++_819: *libsigc++* +++++++++++ The libsigc++ package implements a typesafe callback system for standard C++. *homepage*: https://libsigcplusplus.github.io/libsigcplusplus/ ========== ==================================== version toolchain ========== ==================================== ``2.10.0`` ``GCCcore/6.4.0`` ``2.10.1`` ``GCCcore/7.3.0`` ``2.10.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========== ==================================== .. _list_software_libsigsegv_1071: *libsigsegv* ++++++++++++ GNU libsigsegv is a library for handling page faults in user mode. *homepage*: https://www.gnu.org/software/libsigsegv/ ======== ================= version toolchain ======== ================= ``2.11`` ``GCCcore/6.4.0`` ======== ================= .. _list_software_libSM_471: *libSM* +++++++ X11 Session Management library, which allows for applications to both manage sessions, and make use of session managers to save and restore their state for later use. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= version toolchain ========= ================================================= ``1.2.2`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= .. _list_software_libsndfile_1052: *libsndfile* ++++++++++++ Libsndfile is a C library for reading and writing files containing sampled sound (such as MS Windows WAV and the Apple/SGI AIFF format) through one standard library interface. *homepage*: http://www.mega-nerd.com/libsndfile ========== =========================================================================================== version toolchain ========== =========================================================================================== ``1.0.28`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a`` ========== =========================================================================================== .. _list_software_libsodium_968: *libsodium* +++++++++++ Sodium is a modern, easy-to-use software library for encryption, decryption, signatures, password hashing and more. *homepage*: https://doc.libsodium.org/ ========== ==================================== version toolchain ========== ==================================== ``1.0.6`` ``intel/2016a`` ``1.0.8`` ``foss/2016a`` ``1.0.11`` ``foss/2016b``, ``intel/2016b`` ``1.0.12`` ``GCCcore/6.4.0``, ``intel/2017a`` ``1.0.13`` ``GCCcore/6.4.0``, ``foss/2017a`` ``1.0.16`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.0.17`` ``GCCcore/8.2.0`` ``1.0.18`` ``GCCcore/8.3.0`` ========== ==================================== .. _list_software_LibSoup_702: *LibSoup* +++++++++ libsoup is an HTTP client/server library for GNOME. It uses GObjects and the glib main loop, to integrate well with GNOME applications, and also has a synchronous API, for use in threaded applications. *homepage*: https://wiki.gnome.org/Projects/libsoup ========== ================= version toolchain ========== ================= ``2.66.1`` ``GCCcore/8.2.0`` ========== ================= .. _list_software_libspatialindex_1597: *libspatialindex* +++++++++++++++++ C++ implementation of R*-tree, an MVR-tree and a TPR-tree with C API *homepage*: http://libspatialindex.github.io ========= ====================================================================================== version toolchain ========= ====================================================================================== ``1.8.5`` ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2018a`` ========= ====================================================================================== .. _list_software_libspatialite_1383: *libspatialite* +++++++++++++++ SpatiaLite is an open source library intended to extend the SQLite core to support fully fledged Spatial SQL capabilities. *homepage*: https://www.gaia-gis.it/fossil/libspatialite/home ========== ================= =============================================== version versionsuffix toolchain ========== ================= =============================================== ``4.3.0a`` ``foss/2016b``, ``foss/2018b``, ``intel/2016b`` ``4.3.0a`` ``-Python-3.7.2`` ``foss/2019a`` ========== ================= =============================================== .. _list_software_libssh_645: *libssh* ++++++++ Multiplatform C library implementing the SSHv2 protocol on client and server side *homepage*: https://www.libssh.org ========= ================= version toolchain ========= ================= ``0.9.0`` ``GCCcore/6.4.0`` ========= ================= .. _list_software_LIBSVM_461: *LIBSVM* ++++++++ LIBSVM is an integrated software for support vector classification, (C-SVC, nu-SVC), regression (epsilon-SVR, nu-SVR) and distribution estimation (one-class SVM). It supports multi-class classification. *homepage*: http://www.csie.ntu.edu.tw/~cjlin/libsvm/ ======== ================================ version toolchain ======== ================================ ``3.22`` ``intel/2016b``, ``intel/2017b`` ``3.23`` ``intel/2018b`` ======== ================================ .. _list_software_libtar_638: *libtar* ++++++++ C library for manipulating POSIX tar files *homepage*: https://repo.or.cz/libtar.git ========== ==================================== version toolchain ========== ==================================== ``1.2.20`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ========== ==================================== .. _list_software_libtasn1_798: *libtasn1* ++++++++++ Libtasn1 is the ASN.1 library used by GnuTLS, GNU Shishi and some other packages. It was written by Fabio Fiorina, and has been shipped as part of GnuTLS for some time but is now a proper GNU package. *homepage*: https://www.gnu.org/software/libtasn1/ ======== =================================================== version toolchain ======== =================================================== ``4.7`` ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` ``4.12`` ``GCCcore/5.4.0`` ``4.13`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ======== =================================================== .. _list_software_LibTIFF_576: *LibTIFF* +++++++++ tiff: Library and tools for reading and writing TIFF data files *homepage*: https://libtiff.maptools.org/ ========== ========================================================================================================= version toolchain ========== ========================================================================================================= ``4.0.6`` ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``4.0.7`` ``foss/2016b``, ``intel/2017a`` ``4.0.8`` ``intel/2017a``, ``intel/2017b`` ``4.0.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2017b``, ``intel/2017b``, ``intel/2018.01``, ``intel/2018b`` ``4.0.10`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``4.1.0`` ``GCCcore/8.3.0`` ========== ========================================================================================================= .. _list_software_libtirpc_857: *libtirpc* ++++++++++ Libtirpc is a port of Suns Transport-Independent RPC library to Linux. *homepage*: https://sourceforge.net/projects/libtirpc/ ========= ==================================== version toolchain ========= ==================================== ``1.1.4`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ========= ==================================== .. _list_software_libtool_757: *libtool* +++++++++ GNU libtool is a generic library support script. Libtool hides the complexity of using shared libraries behind a consistent, portable interface. *homepage*: http://www.gnu.org/software/libtool ========= ======================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= version toolchain ========= ======================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= ``2.4.2`` ``GCC/4.8.2``, ``GCC/4.9.2`` ``2.4.5`` ``GCC/4.8.4``, ``GCC/4.9.2`` ``2.4.6`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ========= ======================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================= .. _list_software_libunistring_1306: *libunistring* ++++++++++++++ This library provides functions for manipulating Unicode strings and for manipulating C strings according to the Unicode standard. *homepage*: http://www.gnu.org/software/libunistring/ ========== ======================================================================= version toolchain ========== ======================================================================= ``0.9.3`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` ``0.9.6`` ``GCCcore/5.4.0``, ``foss/2016b``, ``foss/2017a``, ``intel/2016b`` ``0.9.7`` ``GCCcore/6.4.0`` ``0.9.10`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========== ======================================================================= .. _list_software_libunwind_972: *libunwind* +++++++++++ The primary goal of libunwind is to define a portable and efficient C programming interface (API) to determine the call-chain of a program. The API additionally provides the means to manipulate the preserved (callee-saved) state of each call-frame and to resume execution at any point in the call-chain (non-local goto). The API supports both local (same-process) and remote (across-process) operation. As such, the API is useful in a number of applications *homepage*: https://www.nongnu.org/libunwind/ ========= ======================================================================= version toolchain ========= ======================================================================= ``1.1`` ``GCC/4.9.2``, ``foss/2016a``, ``intel/2016b`` ``1.2.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016b`` ``1.3.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ======================================================================= .. _list_software_libutempter_1197: *libutempter* +++++++++++++ libutempter is library that provides an interface for terminal emulators such as screen and xterm to record user sessions to utmp and wtmp files. *homepage*: http://git.altlinux.org/people/ldv/packages/?p=libutempter.git =========== ================== version toolchain =========== ================== ``1.1.6.2`` ``GCC/6.4.0-2.28`` =========== ================== .. _list_software_LibUUID_590: *LibUUID* +++++++++ Portable uuid C library *homepage*: http://sourceforge.net/projects/libuuid/ ========= ========================================================================================================= version toolchain ========= ========================================================================================================= ``1.0.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2016a``, ``intel/2017a``, ``intel/2017b`` ========= ========================================================================================================= .. _list_software_libvdwxc_867: *libvdwxc* ++++++++++ libvdwxc is a general library for evaluating energy and potential for exchange-correlation (XC) functionals from the vdW-DF family that can be used with various of density functional theory (DFT) codes. *homepage*: http://libvdwxc.org ========= ============== version toolchain ========= ============== ``0.3.2`` ``foss/2018b`` ``0.4.0`` ``foss/2019a`` ========= ============== .. _list_software_libwebp_741: *libwebp* +++++++++ WebP is a modern image format that provides superior lossless and lossy compression for images on the web. Using WebP, webmasters and web developers can create smaller, richer images that make the web faster. *homepage*: https://developers.google.com/speed/webp/ ========= ==================================== version toolchain ========= ==================================== ``1.0.0`` ``foss/2018b`` ``1.0.2`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ========= ==================================== .. _list_software_libX11_497: *libX11* ++++++++ X11 client-side library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= version toolchain ========= ================================================= ``1.6.3`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= .. _list_software_libXau_613: *libXau* ++++++++ The libXau package contains a library implementing the X11 Authorization Protocol. This is useful for restricting client access to the display. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= version toolchain ========= ================================================= ``1.0.8`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= .. _list_software_libxc_530: *libxc* +++++++ Libxc is a library of exchange-correlation functionals for density-functional theory. The aim is to provide a portable, well tested and reliable set of exchange and correlation functionals. *homepage*: https://www.tddft.org/programs/libxc ========= ======================================================================================================================================= version toolchain ========= ======================================================================================================================================= ``2.2.2`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` ``2.2.3`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017b``, ``intel/2018a`` ``3.0.0`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``3.0.1`` ``GCC/8.2.0-2.31.1``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` ``4.0.1`` ``foss/2017b``, ``intel/2017b`` ``4.0.3`` ``foss/2016b``, ``foss/2017a`` ``4.2.3`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2017a``, ``intel/2018a``, ``intel/2018b`` ``4.3.4`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ========= ======================================================================================================================================= .. _list_software_libxcb_628: *libxcb* ++++++++ The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. *homepage*: http://xcb.freedesktop.org/ ========== ================================================= version toolchain ========== ================================================= ``1.11.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========== ================================================= .. _list_software_libXcursor_1069: *libXcursor* ++++++++++++ X Cursor management library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========== =============================== version toolchain ========== =============================== ``1.1.14`` ``foss/2016a``, ``intel/2016a`` ========== =============================== .. _list_software_libXdamage_1006: *libXdamage* ++++++++++++ X Damage extension library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= version toolchain ========= ================================================= ``1.1.4`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= .. _list_software_libXdmcp_819: *libXdmcp* ++++++++++ The libXdmcp package contains a library implementing the X Display Manager Control Protocol. This is useful for allowing clients to interact with the X Display Manager. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= version toolchain ========= ================================================= ``1.1.2`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= .. _list_software_libXext_736: *libXext* +++++++++ Common X Extensions library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= version toolchain ========= ================================================= ``1.3.3`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= .. _list_software_libXfixes_942: *libXfixes* +++++++++++ X Fixes extension library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= version toolchain ========= ================================================= ``5.0.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``5.0.2`` ``intel/2016a`` ========= ================================================= .. _list_software_libXfont_838: *libXfont* ++++++++++ X font libary *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =================== ================================================= version versionsuffix toolchain ========= =================== ================================================= ``1.5.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``1.5.1`` ``-freetype-2.6.3`` ``foss/2016a``, ``intel/2016a`` ========= =================== ================================================= .. _list_software_libXft_617: *libXft* ++++++++ X11 client-side library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ======================= =============================== version versionsuffix toolchain ========= ======================= =============================== ``2.3.2`` ``foss/2016a``, ``intel/2016a`` ``2.3.2`` ``-fontconfig-2.11.95`` ``intel/2016a`` ``2.3.2`` ``-freetype-2.6.3`` ``foss/2016a`` ========= ======================= =============================== .. _list_software_libXi_504: *libXi* +++++++ LibXi provides an X Window System client interface to the XINPUT extension to the X protocol. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== version toolchain ========= =============================== ``1.7.6`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_libXinerama_1132: *libXinerama* +++++++++++++ Xinerama multiple monitor library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== version toolchain ========= =============================== ``1.1.3`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_libxkbcommon_1285: *libxkbcommon* ++++++++++++++ xkbcommon is a library to handle keyboard descriptions, including loading them from disk, parsing them and handling their state. It's mainly meant for client toolkits, window systems, and other system applications. *homepage*: http://xkbcommon.org/ ========= =============================== version toolchain ========= =============================== ``0.6.1`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_libxml++_734: *libxml++* ++++++++++ libxml++ is a C++ wrapper for the libxml XML parser library. *homepage*: http://libxmlplusplus.sourceforge.net ========== ======================================================= version toolchain ========== ======================================================= ``2.40.1`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========== ======================================================= .. _list_software_libxml2_698: *libxml2* +++++++++ Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). *homepage*: http://xmlsoft.org/ ========== ================== ================================================================================================================================================================================== version versionsuffix toolchain ========== ================== ================================================================================================================================================================================== ``2.9.2`` ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25`` ``2.9.3`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``2.9.3`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``2.9.4`` ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` ``2.9.4`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``2.9.4`` ``-Python-2.7.13`` ``intel/2017a`` ``2.9.5`` ``GCCcore/6.3.0`` ``2.9.6`` ``GCCcore/6.4.0`` ``2.9.7`` ``GCCcore/6.4.0`` ``2.9.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``2.9.9`` ``GCCcore/8.3.0`` ``2.9.10`` ``GCCcore/9.2.0`` ========== ================== ================================================================================================================================================================================== .. _list_software_libxml2-python_1417: *libxml2-python* ++++++++++++++++ Libxml2 is the XML C parser and toolchain developed for the Gnome project (but usable outside of the Gnome platform). This is the Python binding. *homepage*: http://xmlsoft.org/ ========= ================== ================= version versionsuffix toolchain ========= ================== ================= ``2.9.7`` ``-Python-2.7.14`` ``intel/2018a`` ``2.9.8`` ``-Python-2.7.15`` ``foss/2018b`` ``2.9.8`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========= ================== ================= .. _list_software_libXmu_625: *libXmu* ++++++++ libXmu provides a set of miscellaneous utility convenience functions for X libraries to use. libXmuu is a lighter-weight version that does not depend on libXt or libXext *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== version toolchain ========= =============================== ``1.1.2`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_libXp_511: *libXp* +++++++ libXp provides the X print library. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============== version toolchain ========= =============== ``1.0.3`` ``intel/2016a`` ========= =============== .. _list_software_libXpm_620: *libXpm* ++++++++ libXp provides the X print library. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========== =============================== version toolchain ========== =============================== ``3.5.11`` ``foss/2016a``, ``intel/2016a`` ========== =============================== .. _list_software_libXrandr_934: *libXrandr* +++++++++++ X Resize, Rotate and Reflection extension library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== version toolchain ========= =============================== ``1.5.0`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_libXrender_1039: *libXrender* ++++++++++++ X11 client-side library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= version toolchain ========= ================================================= ``0.9.9`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= .. _list_software_libxslt_770: *libxslt* +++++++++ Libxslt is the XSLT C library developed for the GNOME project (but usable outside of the Gnome platform). *homepage*: http://xmlsoft.org/ ========== ================== ================================================================= version versionsuffix toolchain ========== ================== ================================================================= ``1.1.28`` ``foss/2016a``, ``intel/2016a`` ``1.1.28`` ``-Python-2.7.11`` ``intel/2016a`` ``1.1.29`` ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``1.1.30`` ``GCCcore/6.3.0`` ``1.1.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.1.33`` ``GCCcore/8.2.0`` ``1.1.34`` ``GCCcore/8.3.0`` ========== ================== ================================================================= .. _list_software_libxsmm_764: *libxsmm* +++++++++ LIBXSMM is a library for small dense and small sparse matrix-matrix multiplications targeting Intel Architecture (x86). *homepage*: https://github.com/hfp/libxsmm ========= =============================================================================== version toolchain ========= =============================================================================== ``1.4`` ``intel/2016a`` ``1.4.4`` ``foss/2016b``, ``intel/2016b`` ``1.6.4`` ``foss/2016b``, ``intel/2016b`` ``1.8.2`` ``intel/2017b`` ``1.8.3`` ``foss/2018a``, ``intel/2018a`` ``1.10`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ========= =============================================================================== .. _list_software_libXt_515: *libXt* +++++++ libXt provides the X Toolkit Intrinsics, an abstract widget library upon which other toolkits are based. Xt is the basis for many toolkits, including the Athena widgets (Xaw), and LessTif (a Motif implementation). *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= version toolchain ========= ================================================= ``1.1.5`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= .. _list_software_libXxf86vm_958: *libXxf86vm* ++++++++++++ X11 XFree86 video mode extension library *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== version toolchain ========= =============================== ``1.1.4`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_libyaml_746: *libyaml* +++++++++ LibYAML is a YAML parser and emitter written in C. *homepage*: https://pyyaml.org/wiki/LibYAML ========= =================================================================== version toolchain ========= =================================================================== ``0.1.6`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``0.1.7`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``system`` ``0.2.1`` ``GCCcore/7.3.0``, ``system`` ``0.2.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= =================================================================== .. _list_software_libzip_650: *libzip* ++++++++ libzip is a C library for reading, creating, and modifying zip archives. *homepage*: https://libzip.org/ ========= ================= version toolchain ========= ================= ``1.5.2`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_lifelines_955: *lifelines* +++++++++++ lifelines is a pure Python implementation of the best parts of survival analysis *homepage*: https://lifelines.readthedocs.io ========== ================= ================== version versionsuffix toolchain ========== ================= ================== ``0.22.8`` ``-Python-3.7.2`` ``fosscuda/2019a`` ========== ================= ================== .. _list_software_Lighter_719: *Lighter* +++++++++ Fast and memory-efficient sequencing error corrector *homepage*: https://github.com/mourisl/Lighter ========= ============== version toolchain ========= ============== ``1.1.1`` ``foss/2018a`` ``1.1.2`` ``foss/2018b`` ========= ============== .. _list_software_likwid_644: *likwid* ++++++++ Likwid stands for Like I knew what I am doing. This project contributes easy to use command line tools for Linux to support programmers in developing high performance multi threaded programs. *homepage*: https://github.com/RRZE-HPC/likwid ========= ===================================================================== version toolchain ========= ===================================================================== ``4.0.1`` ``GNU/4.9.3-2.25`` ``4.1.0`` ``GCCcore/4.9.3`` ``4.2.0`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2017a``, ``intel/2017a`` ``4.3.2`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ========= ===================================================================== .. _list_software_LinBox_588: *LinBox* ++++++++ C++ library for exact, high-performance linear algebra *homepage*: http://linalg.org/ ========= ============== version toolchain ========= ============== ``1.4.0`` ``foss/2016a`` ========= ============== .. _list_software_LittleCMS_849: *LittleCMS* +++++++++++ Little CMS intends to be an OPEN SOURCE small-footprint color management engine, with special focus on accuracy and performance. *homepage*: http://www.littlecms.com/ ======= =========================================================================================================================== version toolchain ======= =========================================================================================================================== ``2.7`` ``intel/2016a`` ``2.8`` ``GCCcore/6.4.0``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` ``2.9`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` ======= =========================================================================================================================== .. _list_software_LLVM_315: *LLVM* ++++++ The LLVM Core libraries provide a modern source- and target-independent optimizer, along with code generation support for many popular CPUs (as well as some less common ones!) These libraries are built around a well specified code representation known as the LLVM intermediate representation ("LLVM IR"). The LLVM Core libraries are well documented, and it is particularly easy to invent your own language (or port an existing compiler) to use LLVM as an optimizer and code generator. *homepage*: http://llvm.org/ ========= ======================================================================== version toolchain ========= ======================================================================== ``3.7.1`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``3.8.0`` ``foss/2016a``, ``intel/2016a`` ``3.8.1`` ``GCCcore/4.9.3``, ``foss/2016b``, ``intel/2016b`` ``3.9.0`` ``foss/2016b``, ``intel/2016b`` ``3.9.1`` ``foss/2017a`` ``4.0.0`` ``foss/2017a``, ``intel/2017a`` ``4.0.1`` ``intel/2017a``, ``intel/2017b`` ``5.0.0`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``5.0.1`` ``GCCcore/6.4.0`` ``6.0.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``7.0.0`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``7.0.1`` ``GCCcore/8.2.0`` ``9.0.0`` ``GCCcore/8.3.0`` ========= ======================================================================== .. _list_software_LMDB_287: *LMDB* ++++++ LMDB is a fast, memory-efficient database. With memory-mapped files, it has the read performance of a pure in-memory database while retaining the persistence of standard disk-based databases. *homepage*: https://symas.com/lmdb ========== ================================== version toolchain ========== ================================== ``0.9.18`` ``foss/2016a`` ``0.9.21`` ``GCCcore/6.4.0``, ``intel/2017a`` ``0.9.22`` ``GCCcore/7.3.0`` ``0.9.23`` ``GCCcore/8.2.0`` ``0.9.24`` ``GCCcore/8.3.0`` ========== ================================== .. _list_software_LMfit_476: *LMfit* +++++++ Lmfit provides a high-level interface to non-linear optimization and curve fitting problems for Python *homepage*: https://lmfit.github.io/lmfit-py ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``0.9.9`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== .. _list_software_Lmod_396: *Lmod* ++++++ Lmod is a Lua based module system. Modules allow for dynamic modification of a user's environment under Unix systems. See www.tacc.utexas.edu/tacc-projects/lmod for a complete description. Lmod is a new implementation that easily handles the MODULEPATH Hierarchical problem. It is drop-in replacement for TCL/C modules and reads TCL modulefiles directly. *homepage*: http://sourceforge.net/projects/lmod/ ========= ============================ version toolchain ========= ============================ ``5.2`` ``GCC/4.8.2`` ``5.2.5`` ``GCC/4.8.2`` ``5.3`` ``GCC/4.8.2`` ``5.4`` ``GCC/4.8.2`` ``5.4.2`` ``GCC/4.8.2`` ``5.5`` ``GCC/4.8.2`` ``5.5.1`` ``GCC/4.8.2`` ``5.6`` ``GCC/4.8.2`` ``5.7`` ``GCC/4.8.2`` ``5.8`` ``GCC/4.8.2`` ``5.8.5`` ``GCC/4.8.2`` ``5.9`` ``GCC/4.8.2``, ``GCC/4.8.4`` ``6.4.2`` ``system`` ``7.3`` ``system`` ========= ============================ .. _list_software_LocARNA_576: *LocARNA* +++++++++ LocARNA is a collection of alignment tools for the structural analysis of RNA. Given a set of RNA sequences, LocARNA simultaneously aligns and predicts common structures for your RNAs. In this way, LocARNA performs Sankoff-like alignment and is in particular suited for analyzing sets of related RNAs without known common structure. *homepage*: http://www.bioinf.uni-freiburg.de/Software/LocARNA/ =========== ================= ============== version versionsuffix toolchain =========== ================= ============== ``1.9.2`` ``foss/2016b`` ``1.9.2.2`` ``-Python-3.6.6`` ``foss/2018b`` =========== ================= ============== .. _list_software_LoFreq_585: *LoFreq* ++++++++ Fast and sensitive variant calling from next-gen sequencing data *homepage*: http://csb5.github.io/lofreq =========== ================== ================================================ version versionsuffix toolchain =========== ================== ================================================ ``2.1.2`` ``-Python-2.7.12`` ``intel/2016b`` ``2.1.3.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` =========== ================== ================================================ .. _list_software_Log-Log4perl_1112: *Log-Log4perl* ++++++++++++++ Log4perl *homepage*: https://metacpan.org/pod/Log::Log4perl ======== ============== version toolchain ======== ============== ``1.47`` ``foss/2016a`` ======== ============== .. _list_software_LOHHLA_440: *LOHHLA* ++++++++ LOHHLA, Loss Of Heterozygosity in Human Leukocyte Antigen, a computational tool to evaluate HLA loss using next-generation sequencing data. *homepage*: https://bitbucket.org/mcgranahanlab/lohhla ============== ============= ============== version versionsuffix toolchain ============== ============= ============== ``2018.11.05`` ``-R-3.5.1`` ``foss/2018b`` ============== ============= ============== .. _list_software_Loki_399: *Loki* ++++++ Loki is a C++ library of designs, containing flexible implementations of common design patterns and idioms. *homepage*: http://loki-lib.sourceforge.net/ ========= ================================================================================= version toolchain ========= ================================================================================= ``0.1.7`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2018a`` ========= ================================================================================= .. _list_software_Longshot_846: *Longshot* ++++++++++ Longshot is a variant calling tool for diploid genomes using long error prone reads such as Pacific Biosciences (PacBio) SMRT and Oxford Nanopore Technologies (ONT). It takes as input an aligned BAM file and outputs a phased VCF file with variants and haplotype information. It can also output haplotype-separated BAM files that can be used for downstream analysis. Currently, it only calls single nucleotide variants (SNVs). *homepage*: https://github.com/pjedge/longshot ========= ================= version toolchain ========= ================= ``0.3.4`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_lpsolve_773: *lpsolve* +++++++++ Mixed Integer Linear Programming (MILP) solver *homepage*: https://sourceforge.net/projects/lpsolve/ =========== ===================================================================================================================================================================== version toolchain =========== ===================================================================================================================================================================== ``5.5.2.5`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2017a``, ``intel/2018b`` =========== ===================================================================================================================================================================== .. _list_software_lrslib_648: *lrslib* ++++++++ lrslib is a self-contained ANSI C implementation of the reverse search algorithm for vertex enumeration/convex hull problems *homepage*: http://cgm.cs.mcgill.ca/~avis/C/lrs.html ======= =============== version toolchain ======= =============== ``6.2`` ``intel/2018b`` ======= =============== .. _list_software_LS-PrePost_921: *LS-PrePost* ++++++++++++ LS-PrePost is an advanced pre and post-processor that is delivered free with LS-DYNA. *homepage*: http://lstc.com/products/ls-prepost ======= ============= ========== version versionsuffix toolchain ======= ============= ========== ``4.6`` ``-centos6`` ``system`` ``4.6`` ``-centos7`` ``system`` ======= ============= ========== .. _list_software_LSMS_319: *LSMS* ++++++ LSMS benchmark, part of CORAL suite *homepage*: https://asc.llnl.gov/CORAL-benchmarks/#lsms ============ ============== version toolchain ============ ============== ``3_rev237`` ``foss/2016a`` ============ ============== .. _list_software_Lua_290: *Lua* +++++ Lua is a powerful, fast, lightweight, embeddable scripting language. Lua combines simple procedural syntax with powerful data description constructs based on associative arrays and extensible semantics. Lua is dynamically typed, runs by interpreting bytecode for a register-based virtual machine, and has automatic memory management with incremental garbage collection, making it ideal for configuration, scripting, and rapid prototyping. *homepage*: http://www.lua.org/ =========== ======================================== version toolchain =========== ======================================== ``5.1.4-5`` ``GCC/4.8.2`` ``5.1.4-8`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``system`` ``5.1.5`` ``GCCcore/7.3.0`` ``5.2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``5.3.4`` ``GCCcore/7.2.0``, ``system`` ``5.3.5`` ``GCCcore/8.2.0``, ``system`` =========== ======================================== .. _list_software_LuaJIT_521: *LuaJIT* ++++++++ LuaJIT is a Just-In-Time Compiler (JIT) for the Lua programming language. Lua is a powerful, dynamic and light-weight programming language. It may be embedded or used as a general-purpose, stand-alone language. *homepage*: http://luajit.org/ ========= ============= version toolchain ========= ============= ``2.0.2`` ``GCC/4.9.2`` ========= ============= .. _list_software_Lucene-Geo-Gazetteer_1916: *Lucene-Geo-Gazetteer* ++++++++++++++++++++++ A command line gazetteer built around the Geonames.org dataset, that uses the Apache Lucene library to create a searchable gazetteer. *homepage*: https://github.com/chrismattmann/lucene-geo-gazetteer ============ ========== version toolchain ============ ========== ``20170718`` ``system`` ============ ========== .. _list_software_LUMPY_407: *LUMPY* +++++++ A probabilistic framework for structural variant discovery. *homepage*: https://github.com/arq5x/lumpy-sv ========== ============== version toolchain ========== ============== ``0.2.13`` ``foss/2016b`` ========== ============== .. _list_software_LUSCUS_479: *LUSCUS* ++++++++ Luscus is the program for graphical display and editing of molecular systems. *homepage*: https://sourceforge.net/projects/luscus/ ========= =============================== version toolchain ========= =============================== ``0.8.6`` ``foss/2018b``, ``intel/2018a`` ========= =============================== .. _list_software_lwgrp_556: *lwgrp* +++++++ The Light-weight Group Library provides methods for MPI codes to quickly create and destroy process groups *homepage*: https://github.com/llnl/lwgrp ========= ================================ version toolchain ========= ================================ ``1.0.2`` ``gompi/2019a``, ``iimpi/2019a`` ========= ================================ .. _list_software_lxml_445: *lxml* ++++++ The lxml XML toolkit is a Pythonic binding for the C libraries libxml2 and libxslt. *homepage*: https://lxml.de/ ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``3.5.0`` ``-Python-2.7.11`` ``intel/2016a`` ``3.6.0`` ``-Python-2.7.11`` ``intel/2016a`` ``3.6.4`` ``-Python-2.7.12`` ``intel/2016b`` ``4.0.0`` ``-Python-2.7.13`` ``intel/2017a`` ``4.1.1`` ``-Python-2.7.14`` ``intel/2017b`` ``4.2.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``4.2.0`` ``-Python-3.6.4`` ``intel/2018a`` ``4.2.5`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``4.2.5`` ``-Python-3.6.6`` ``foss/2018b`` ``4.3.3`` ``GCCcore/8.2.0`` ``4.4.2`` ``GCCcore/8.3.0`` ========= ================== =============================== .. _list_software_lynx_459: *lynx* ++++++ lynx is an alphanumeric display oriented World-Wide Web Client *homepage*: http://lynx.browser.org/ ========= ============= ============== version versionsuffix toolchain ========= ============= ============== ``2.8.9`` ``-develop`` ``foss/2016b`` ========= ============= ============== .. _list_software_lz4_282: *lz4* +++++ LZ4 is lossless compression algorithm, providing compression speed at 400 MB/s per core. It features an extremely fast decoder, with speed in multiple GB/s per core. *homepage*: https://lz4.github.io/lz4/ ========= ==================================== version toolchain ========= ==================================== ``1.8.2`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0`` ``1.9.0`` ``GCCcore/7.3.0`` ``1.9.1`` ``GCCcore/8.2.0`` ``1.9.2`` ``GCCcore/8.3.0`` ========= ==================================== .. _list_software_LZO_245: *LZO* +++++ Portable lossless data compression library *homepage*: http://www.oberhumer.com/opensource/lzo/ ======== ========================================================================================================================================================= version toolchain ======== ========================================================================================================================================================= ``2.09`` ``intel/2016b``, ``intel/2017b`` ``2.10`` ``GCCcore/6.4.0``, ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017a`` ======== ========================================================================================================================================================= .. _list_software_letter_m: *M* --- :ref:`list_software_M4_129` - :ref:`list_software_MACH_281` - :ref:`list_software_MACS2_342` - :ref:`list_software_maeparser_960` - :ref:`list_software_MAFFT_366` - :ref:`list_software_magick_620` - :ref:`list_software_magma_515` - :ref:`list_software_MAGMA_355` - :ref:`list_software_MagresPython_1249` - :ref:`list_software_mahotas_749` - :ref:`list_software_MAJIQ_370` - :ref:`list_software_make_414` - :ref:`list_software_makedepend_1038` - :ref:`list_software_makedepf90_934` - :ref:`list_software_Mako_392` - :ref:`list_software_Maple_495` - :ref:`list_software_MapSplice_894` - :ref:`list_software_Maq_287` - :ref:`list_software_MariaDB_624` - :ref:`list_software_MariaDB-connector-c_1784` - :ref:`list_software_Mash_393` - :ref:`list_software_MaSuRCA_588` - :ref:`list_software_Mathematica_1118` - :ref:`list_software_MathGL_541` - :ref:`list_software_MATIO_378` - :ref:`list_software_MATLAB_433` - :ref:`list_software_MATLAB-Engine_1076` - :ref:`list_software_matplotlib_1080` - :ref:`list_software_MATSim_523` - :ref:`list_software_Maven_503` - :ref:`list_software_mawk_432` - :ref:`list_software_MaxBin_575` - :ref:`list_software_MaxQuant_815` - :ref:`list_software_mayavi_647` - :ref:`list_software_mc_208` - :ref:`list_software_MCL_220` - :ref:`list_software_MCR_226` - :ref:`list_software_MDBM_288` - :ref:`list_software_MDSplus_680` - :ref:`list_software_mdtest_657` - :ref:`list_software_MDTraj_546` - :ref:`list_software_medaka_611` - :ref:`list_software_Meep_391` - :ref:`list_software_MEGA_282` - :ref:`list_software_MEGACC_416` - :ref:`list_software_MEGAHIT_511` - :ref:`list_software_Meld_386` - :ref:`list_software_MEME_292` - :ref:`list_software_memkind_741` - :ref:`list_software_memory-profiler_1577` - :ref:`list_software_meRanTK_658` - :ref:`list_software_MERCKX_458` - :ref:`list_software_Mercurial_932` - :ref:`list_software_Mesa_390` - :ref:`list_software_meshio_645` - :ref:`list_software_Meson_514` - :ref:`list_software_Mesquite_845` - :ref:`list_software_MetaBAT_606` - :ref:`list_software_MetaboAnalystR_1414` - :ref:`list_software_MetaGeneAnnotator_1724` - :ref:`list_software_Metal_499` - :ref:`list_software_MetaPhlAn2_908` - :ref:`list_software_metaWRAP_737` - :ref:`list_software_Metaxa2_658` - :ref:`list_software_MethylDackel_1207` - :ref:`list_software_methylpy_892` - :ref:`list_software_METIS_386` - :ref:`list_software_mhcflurry_988` - :ref:`list_software_MiGEC_389` - :ref:`list_software_MIGRATE-N_644` - :ref:`list_software_MINC_295` - :ref:`list_software_Miniconda2_964` - :ref:`list_software_Miniconda3_965` - :ref:`list_software_minieigen_949` - :ref:`list_software_Minimac4_754` - :ref:`list_software_minimap2_797` - :ref:`list_software_MinPath_689` - :ref:`list_software_MIRA_297` - :ref:`list_software_miRDeep2_728` - :ref:`list_software_MiXCR_419` - :ref:`list_software_mkl-dnn_689` - :ref:`list_software_mkl-service_1122` - :ref:`list_software_MLC_220` - :ref:`list_software_Mmg_289` - :ref:`list_software_MMSEQ_387` - :ref:`list_software_MMseqs2_648` - :ref:`list_software_modred_635` - :ref:`list_software_Molcas_607` - :ref:`list_software_Molden_607` - :ref:`list_software_Molekel_713` - :ref:`list_software_molmod_648` - :ref:`list_software_Molpro_633` - :ref:`list_software_Mono_409` - :ref:`list_software_mordecai_836` - :ref:`list_software_mosdepth_868` - :ref:`list_software_Mothur_639` - :ref:`list_software_motif_543` - :ref:`list_software_MotionCor2_972` - :ref:`list_software_MoviePy_713` - :ref:`list_software_MPC_224` - :ref:`list_software_MPFR_309` - :ref:`list_software_mpi4py_611` - :ref:`list_software_MPICH_369` - :ref:`list_software_MPICH2_419` - :ref:`list_software_mpifileutils_1303` - :ref:`list_software_mpiP_406` - :ref:`list_software_MPJ-Express_1022` - :ref:`list_software_mpmath_647` - :ref:`list_software_MrBayes_691` - :ref:`list_software_MRIcron_666` - :ref:`list_software_MRtrix_614` - :ref:`list_software_MSM_237` - :ref:`list_software_MSPC_307` - :ref:`list_software_msprime_765` - :ref:`list_software_MTL4_289` - :ref:`list_software_MultiNest_933` - :ref:`list_software_MultiQC_671` - :ref:`list_software_Multiwfn_854` - :ref:`list_software_MUMmer_563` - :ref:`list_software_MUMPS_402` - :ref:`list_software_muParser_847` - :ref:`list_software_MuPeXI_536` - :ref:`list_software_MUSCLE_457` - :ref:`list_software_MuSiC_449` - :ref:`list_software_MuTect_594` - :ref:`list_software_mutil_555` - :ref:`list_software_MVAPICH2_570` - :ref:`list_software_MXNet_460` - :ref:`list_software_mygene_645` - :ref:`list_software_MyMediaLite_1076` - :ref:`list_software_mympingpong_1205` - :ref:`list_software_mypy_463` - :ref:`list_software_MySQL_438` - :ref:`list_software_MySQL-python_1157` - :ref:`list_software_mysqlclient_1205` .. _list_software_M4_129: *M4* ++++ GNU M4 is an implementation of the traditional Unix macro processor. It is mostly SVR4 compatible although it has some extensions (for example, handling more than 9 positional parameters to macros). GNU M4 also has built-in functions for including files, running shell commands, doing arithmetic, etc. *homepage*: http://www.gnu.org/software/m4/m4.html ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.4.16`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``system`` ``1.4.17`` ``GCC/4.8.2``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCC/5.2.0``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25``, ``GNU/5.1.0-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.4.18`` ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/system``, ``system`` ========== =========================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_MACH_281: *MACH* ++++++ MACH 1.0 is a Markov Chain based haplotyper that can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals. *homepage*: http://csg.sph.umich.edu/abecasis/MACH/ ========== ========== version toolchain ========== ========== ``1.0.18`` ``system`` ========== ========== .. _list_software_MACS2_342: *MACS2* +++++++ Model Based Analysis for ChIP-Seq data *homepage*: https://github.com/taoliu/MACS/ ================== ================== =============================== version versionsuffix toolchain ================== ================== =============================== ``2.1.1.20160309`` ``-Python-2.7.14`` ``intel/2017b`` ``2.1.2.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2.1.2.1`` ``-Python-2.7.15`` ``intel/2019a`` ``2.2.5`` ``-Python-3.6.6`` ``foss/2018b`` ================== ================== =============================== .. _list_software_maeparser_960: *maeparser* +++++++++++ maeparser is a parser for Schrodinger Maestro files. *homepage*: https://github.com/schrodinger/maeparser ========= ================================ version toolchain ========= ================================ ``1.2.2`` ``gompi/2019a``, ``iimpi/2019a`` ========= ================================ .. _list_software_MAFFT_366: *MAFFT* +++++++ MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of multiple alignment methods, L-INS-i (accurate; for alignment of <∼200 sequences), FFT-NS-2 (fast; for alignment of <∼10,000 sequences), etc. *homepage*: https://mafft.cbrc.jp/alignment/software/source.html ========= ==================== ==================== version versionsuffix toolchain ========= ==================== ==================== ``7.305`` ``-with-extensions`` ``foss/2016b`` ``7.397`` ``-with-extensions`` ``intel/2018a`` ``7.427`` ``-with-extensions`` ``intel/2018b`` ``7.429`` ``-with-extensions`` ``GCC/8.2.0-2.31.1`` ========= ==================== ==================== .. _list_software_magick_620: *magick* ++++++++ R bindings to the open-source image processing library ImageMagick *homepage*: https://cran.r-project.org/web/packages/magick/ ======= ============= ============== version versionsuffix toolchain ======= ============= ============== ``2.0`` ``-R-3.5.1`` ``foss/2018b`` ======= ============= ============== .. _list_software_magma_515: *magma* +++++++ The MAGMA project aims to develop a dense linear algebra library similar to LAPACK but for heterogeneous/hybrid architectures, starting with current Multicore+GPU systems. *homepage*: https://icl.cs.utk.edu/magma/ ========= ================ ======================================= version versionsuffix toolchain ========= ================ ======================================= ``2.3.0`` ``fosscuda/2017b``, ``intelcuda/2017b`` ``2.3.0`` ``-CUDA-9.1.85`` ``foss/2018a`` ``2.4.0`` ``fosscuda/2018b`` ``2.5.0`` ``fosscuda/2018b`` ``2.5.1`` ``fosscuda/2019a``, ``fosscuda/2019b`` ========= ================ ======================================= .. _list_software_MAGMA_355: *MAGMA* +++++++ MAGMA is a tool for gene analysis and generalized gene-set analysis of GWAS data. It can be used to analyse both raw genotype data as well as summary SNP p-values from a previous GWAS or meta-analysis. *homepage*: https://ctg.cncr.nl/software/magma ========= ============== version toolchain ========= ============== ``1.07b`` ``foss/2018b`` ========= ============== .. _list_software_MagresPython_1249: *MagresPython* ++++++++++++++ MagresPython is a Python library for parsing the CCP-NC ab-initio magnetic resonance file format. This is used in the latest version of the CASTEP and Quantum ESPRESSO (PWSCF) codes. *homepage*: http://tfgg.me/magres-python ============ ================== ============== version versionsuffix toolchain ============ ================== ============== ``20160329`` ``-Python-2.7.15`` ``foss/2018b`` ============ ================== ============== .. _list_software_mahotas_749: *mahotas* +++++++++ Mahotas is a computer vision and image processing library for Python *homepage*: http://mahotas.readthedocs.io/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.4.3`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== .. _list_software_MAJIQ_370: *MAJIQ* +++++++ MAJIQ and Voila are two software packages that together detect, quantify, and visualize local splicing variations (LSV) from RNA-Seq data. *homepage*: https://majiq.biociphers.org ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``1.1.1`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== .. _list_software_make_414: *make* ++++++ GNU version of make utility *homepage*: https://www.gnu.org/software/make/make.html ========= ===================================== version toolchain ========= ===================================== ``3.82`` ``GCC/4.8.2`` ``4.1`` ``GCC/4.9.2`` ``4.2.1`` ``GCC/7.3.0-2.30``, ``GCCcore/8.3.0`` ========= ===================================== .. _list_software_makedepend_1038: *makedepend* ++++++++++++ The makedepend package contains a C-preprocessor like utility to determine build-time dependencies. *homepage*: https://linux.die.net/man/1/makedepend ========= ======================================================================================= version toolchain ========= ======================================================================================= ``1.0.5`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``1.0.6`` ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` ========= ======================================================================================= .. _list_software_makedepf90_934: *makedepf90* ++++++++++++ Makedepf90 is a program for automatic creation of Makefile-style dependency lists for Fortran source code. *homepage*: https://linux.die.net/man/1/makedepf90 ========= ============== version toolchain ========= ============== ``2.8.8`` ``foss/2017a`` ========= ============== .. _list_software_Mako_392: *Mako* ++++++ A super-fast templating language that borrows the best ideas from the existing templating languages *homepage*: http://www.makotemplates.org ========= ================== ================================================================================================================================================================= version versionsuffix toolchain ========= ================== ================================================================================================================================================================= ``1.0.4`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``1.0.6`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` ``1.0.7`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``intel/2017b``, ``intel/2018.01``, ``intel/2018a``, ``intelcuda/2017b``, ``iomkl/2018a`` ``1.0.7`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``1.0.7`` ``-Python-3.6.4`` ``intel/2018a`` ``1.0.7`` ``-Python-3.6.6`` ``fosscuda/2018b`` ``1.0.8`` ``GCCcore/8.2.0`` ``1.1.0`` ``GCCcore/8.3.0`` ========= ================== ================================================================================================================================================================= .. _list_software_Maple_495: *Maple* +++++++ Maple combines the world's most powerful mathematical computation engine with an intuitive, 'clickable' user interface. *homepage*: http://www.maplesoft.com/products/maple/ ========== ========== version toolchain ========== ========== ``15`` ``system`` ``2017.2`` ``system`` ========== ========== .. _list_software_MapSplice_894: *MapSplice* +++++++++++ MapSplice is a software for mapping RNA-seq data to reference genome for splice junction discovery that depends only on reference genome, and not on any further annotations. *homepage*: http://www.netlab.uky.edu/p/bioinfo/MapSplice2 ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``2.2.1`` ``-Python-2.7.12`` ``foss/2016b`` ``2.2.1`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============== .. _list_software_Maq_287: *Maq* +++++ Maq is a software that builds mapping assemblies from short reads generated by the next-generation sequencing machines. *homepage*: http://maq.sourceforge.net/maq-man.shtml ========= ========== version toolchain ========= ========== ``0.7.0`` ``system`` ========= ========== .. _list_software_MariaDB_624: *MariaDB* +++++++++ MariaDB An enhanced, drop-in replacement for MySQL. *homepage*: https://mariadb.org/ =========== =============================== version toolchain =========== =============================== ``10.0.21`` ``GNU/4.9.3-2.25`` ``10.1.13`` ``intel/2016a`` ``10.1.14`` ``foss/2016a``, ``intel/2016a`` ``10.1.17`` ``intel/2016b`` ``10.1.24`` ``intel/2017a`` ``10.2.11`` ``foss/2017b``, ``intel/2017b`` ``10.3.7`` ``intel/2018a`` ``10.3.10`` ``foss/2018b`` ``10.3.14`` ``foss/2019a`` =========== =============================== .. _list_software_MariaDB-connector-c_1784: *MariaDB-connector-c* +++++++++++++++++++++ MariaDB Connector/C is used to connect applications developed in C/C++ to MariaDB and MySQL databases. *homepage*: https://downloads.mariadb.org/connector-c/ ========= ================================= version toolchain ========= ================================= ``2.3.4`` ``foss/2017b``, ``intel/2017b`` ``2.3.5`` ``intel/2018a``, ``iomkl/2018a`` ``2.3.7`` ``GCCcore/8.2.0``, ``foss/2018b`` ========= ================================= .. _list_software_Mash_393: *Mash* ++++++ Fast genome and metagenome distance estimation using MinHash *homepage*: http://mash.readthedocs.org ======= ============== version toolchain ======= ============== ``2.0`` ``foss/2018a`` ``2.1`` ``foss/2018b`` ======= ============== .. _list_software_MaSuRCA_588: *MaSuRCA* +++++++++ MaSuRCA is whole genome assembly software. It combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches. MaSuRCA can assemble data sets containing only short reads from Illumina sequencing or a mixture of short reads and long reads (Sanger, 454, Pacbio and Nanopore). *homepage*: http://www.genome.umd.edu/masurca.html ========= ================ ============== version versionsuffix toolchain ========= ================ ============== ``3.2.2`` ``foss/2016a`` ``3.2.2`` ``-Perl-5.26.0`` ``foss/2017b`` ``3.2.4`` ``foss/2018a`` ``3.2.5`` ``-Perl-5.26.0`` ``foss/2017b`` ``3.3.1`` ``-Perl-5.28.0`` ``foss/2018b`` ========= ================ ============== .. _list_software_Mathematica_1118: *Mathematica* +++++++++++++ Mathematica is a computational software program used in many scientific, engineering, mathematical and computing fields. *homepage*: http://www.wolfram.com/mathematica ========== ========== version toolchain ========== ========== ``9.0.1`` ``system`` ``10.0.2`` ``system`` ``10.1.0`` ``system`` ``10.4.1`` ``system`` ``11.0.1`` ``system`` ``11.1.1`` ``system`` ``11.3.0`` ``system`` ``12.0.0`` ``system`` ========== ========== .. _list_software_MathGL_541: *MathGL* ++++++++ MathGL is ... a library for making high-quality scientific graphics under Linux and Windows; a library for the fast data plotting and data processing of large data arrays; a library for working in window and console modes and for easy embedding into other programs; a library with large and growing set of graphics. *homepage*: http://mathgl.sourceforge.net/doc_en/Main.html ========= ============== version toolchain ========= ============== ``2.4.1`` ``foss/2018a`` ========= ============== .. _list_software_MATIO_378: *MATIO* +++++++ matio is an C library for reading and writing Matlab MAT files. *homepage*: http://sourceforge.net/projects/matio/ ========== ================= version toolchain ========== ================= ``1.5.9`` ``GCCcore/5.4.0`` ``1.5.11`` ``foss/2017b`` ``1.5.12`` ``GCCcore/6.4.0`` ========== ================= .. _list_software_MATLAB_433: *MATLAB* ++++++++ MATLAB is a high-level language and interactive environment that enables you to perform computationally intensive tasks faster than with traditional programming languages such as C, C++, and Fortran. *homepage*: http://www.mathworks.com/products/matlab ========= ========== version toolchain ========= ========== ``2012b`` ``system`` ``2013b`` ``system`` ``2015a`` ``system`` ``2016a`` ``system`` ``2017a`` ``system`` ``2018b`` ``system`` ========= ========== .. _list_software_MATLAB-Engine_1076: *MATLAB-Engine* +++++++++++++++ The MATLAB Engine API for Python provides a package for Python to call MATLAB as a computational engine. *homepage*: https://www.mathworks.com/help/matlab/matlab-engine-for-python.html ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``2018b`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2018b`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ========= ================== =============================== .. _list_software_matplotlib_1080: *matplotlib* ++++++++++++ matplotlib is a python 2D plotting library which produces publication quality figures in a variety of hardcopy formats and interactive environments across platforms. matplotlib can be used in python scripts, the python and ipython shell, web application servers, and six graphical user interface toolkits. *homepage*: https://matplotlib.org ========= ================================= ======================================================================== version versionsuffix toolchain ========= ================================= ======================================================================== ``1.4.3`` ``-Python-2.7.12`` ``intel/2016b`` ``1.5.1`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``1.5.1`` ``-Python-2.7.11-freetype-2.6.3`` ``foss/2016a``, ``intel/2016a`` ``1.5.1`` ``-Python-2.7.12`` ``intel/2016b`` ``1.5.1`` ``-Python-3.5.1`` ``foss/2016a``, ``intel/2016a`` ``1.5.1`` ``-Python-3.5.2`` ``intel/2016b`` ``1.5.2`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``1.5.2`` ``-Python-3.5.2`` ``intel/2016b`` ``1.5.3`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``1.5.3`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` ``2.0.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``2.0.0`` ``-Python-2.7.13`` ``intel/2017a`` ``2.0.1`` ``-Python-3.6.1`` ``intel/2017a`` ``2.0.2`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` ``2.0.2`` ``-Python-2.7.13-Qt-4.8.7`` ``intel/2017a`` ``2.0.2`` ``-Python-2.7.13-libpng-1.6.29`` ``intel/2017a`` ``2.0.2`` ``-Python-3.6.1`` ``foss/2017a`` ``2.0.2`` ``-Python-3.6.1-libpng-1.6.29`` ``intel/2017a`` ``2.1.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``2.1.0`` ``-Python-3.6.2`` ``foss/2017b`` ``2.1.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``2.1.1`` ``-Python-2.7.14`` ``intel/2017b`` ``2.1.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``2.1.2`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``2.1.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018.02``, ``iomkl/2018a`` ``2.2.3`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``2.2.3`` ``-Python-3.6.6`` ``intel/2018b`` ``2.2.4`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` ``3.0.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.0.2`` ``-Python-3.6.6`` ``foss/2018b`` ``3.0.3`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` ``3.1.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========= ================================= ======================================================================== .. _list_software_MATSim_523: *MATSim* ++++++++ MATSim is an open-source framework to implement large-scale agent-based transport simulations. *homepage*: http://www.matsim.org/ ========= =================== =============== version versionsuffix toolchain ========= =================== =============== ``0.8.1`` ``-Java-1.8.0_112`` ``intel/2016b`` ========= =================== =============== .. _list_software_Maven_503: *Maven* +++++++ Binary maven install, Apache Maven is a software project management and comprehension tool. Based on the concept of a project object model (POM), Maven can manage a project's build, reporting and documentation from a central piece of information. *homepage*: https://maven.apache.org/index.html ========= ========== version toolchain ========= ========== ``3.2.3`` ``system`` ``3.3.3`` ``system`` ``3.3.9`` ``system`` ``3.5.0`` ``system`` ``3.5.2`` ``system`` ``3.6.0`` ``system`` ========= ========== .. _list_software_mawk_432: *mawk* ++++++ mawk is an interpreter for the AWK Programming Language. *homepage*: https://invisible-island.net/mawk/ ================== ================================================================================================= version toolchain ================== ================================================================================================= ``1.3.4-20141206`` ``GCC/4.9.2`` ``1.3.4-20171017`` ``foss/2018a``, ``foss/2018b``, ``foss/2019a``, ``intel/2018a``, ``intel/2018b``, ``intel/2019a`` ================== ================================================================================================= .. _list_software_MaxBin_575: *MaxBin* ++++++++ MaxBin is software for binning assembled metagenomic sequences based on an Expectation-Maximization algorithm. *homepage*: https://downloads.jbei.org/data/microbial_communities/MaxBin/MaxBin.html ========= ================ ==================== version versionsuffix toolchain ========= ================ ==================== ``2.2.6`` ``-Perl-5.28.0`` ``foss/2018b`` ``2.2.7`` ``-Perl-5.28.1`` ``GCC/8.2.0-2.31.1`` ========= ================ ==================== .. _list_software_MaxQuant_815: *MaxQuant* ++++++++++ MaxQuant is a quantitative proteomics software package designed for analyzing large mass-spectrometric data sets. It is specifically aimed at high-resolution MS data. Several labeling techniques as well as label-free quantification are supported. *homepage*: https://maxquant.org/maxquant/ ============= ============== version toolchain ============= ============== ``1.6.10.43`` ``foss/2018b`` ============= ============== .. _list_software_mayavi_647: *mayavi* ++++++++ The Mayavi scientific data 3-dimensional visualizer *homepage*: http://code.enthought.com/projects/mayavi/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``4.4.4`` ``-Python-2.7.11`` ``intel/2016a`` ``4.7.1`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================== =============== .. _list_software_mc_208: *mc* ++++ mc-4.6.1: User-friendly file manager and visual shell *homepage*: https://www.midnight-commander.org/ ========== ============= version toolchain ========== ============= ``4.8.13`` ``GCC/4.9.2`` ========== ============= .. _list_software_MCL_220: *MCL* +++++ The MCL algorithm is short for the Markov Cluster Algorithm, a fast and scalable unsupervised cluster algorithm for graphs (also known as networks) based on simulation of (stochastic) flow in graphs. *homepage*: http://micans.org/mcl/ ========== ================ =============================== version versionsuffix toolchain ========== ================ =============================== ``02.063`` ``intel/2016b`` ``14.137`` ``foss/2016a``, ``intel/2016b`` ``14.137`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` ``14.137`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` ========== ================ =============================== .. _list_software_MCR_226: *MCR* +++++ The MATLAB Runtime is a standalone set of shared libraries that enables the execution of compiled MATLAB applications or components on computers that do not have MATLAB installed. *homepage*: http://www.mathworks.com/products/compiler/mcr/ ========== ========== version toolchain ========== ========== ``R2013a`` ``system`` ``R2013b`` ``system`` ``R2014a`` ``system`` ``R2014b`` ``system`` ``R2015a`` ``system`` ``R2015b`` ``system`` ``R2016a`` ``system`` ``R2016b`` ``system`` ``R2018a`` ``system`` ``R2018b`` ``system`` ``R2019a`` ``system`` ========== ========== .. _list_software_MDBM_288: *MDBM* ++++++ MDBM is a super-fast memory-mapped key/value store *homepage*: https://github.com/yahoo/mdbm ========== ================= version toolchain ========== ================= ``4.13.0`` ``GCCcore/6.4.0`` ========== ================= .. _list_software_MDSplus_680: *MDSplus* +++++++++ MDSplus is a set of software tools for data acquisition and storage and a methodology for management of complex scientific data. *homepage*: http://mdsplus.org/ ========== ================================ ============== version versionsuffix toolchain ========== ================================ ============== ``7.0.67`` ``-Java-1.7.0_79-Python-2.7.11`` ``foss/2016a`` ``7.46.1`` ``foss/2018a`` ========== ================================ ============== .. _list_software_mdtest_657: *mdtest* ++++++++ mdtest is an MPI-coordinated metadata benchmark test that performs open/stat/close operations on files and directories and then reports the performance. *homepage*: http://sourceforge.net/projects/mdtest/ ========= =============== version toolchain ========= =============== ``1.9.3`` ``intel/2017a`` ========= =============== .. _list_software_MDTraj_546: *MDTraj* ++++++++ Read, write and analyze MD trajectories with only a few lines of Python code. *homepage*: http://mdtraj.org ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``1.9.1`` ``-Python-3.6.3`` ``intel/2017b`` ``1.9.2`` ``-Python-3.6.6`` ``intel/2018b`` ``1.9.3`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================= =============== .. _list_software_medaka_611: *medaka* ++++++++ medaka is a tool to create a consensus sequence of nanopore sequencing data. *homepage*: https://nanoporetech.github.io/medaka ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``0.4.3`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== .. _list_software_Meep_391: *Meep* ++++++ Meep (or MEEP) is a free finite-difference time-domain (FDTD) simulation software package developed at MIT to model electromagnetic systems. *homepage*: http://ab-initio.mit.edu/wiki/index.php/Meep ======= ============== version toolchain ======= ============== ``1.3`` ``foss/2016a`` ======= ============== .. _list_software_MEGA_282: *MEGA* ++++++ MEGA-CC (Molecular Evolutionary Genetics Analysis Computational Core) is an integrated suite of tools for statistics-based comparative analysis of molecular sequence data based on evolutionary principles. *homepage*: http://www.megasoftware.net/ ============ ========== version toolchain ============ ========== ``7.0.20-1`` ``system`` ============ ========== .. _list_software_MEGACC_416: *MEGACC* ++++++++ MEGA-Computing Core - Sophisticated and user-friendly software suite for analyzing DNA and protein sequence data from species and populations. *homepage*: http://www.megasoftware.net ============ ========== version toolchain ============ ========== ``7.0.18-1`` ``system`` ============ ========== .. _list_software_MEGAHIT_511: *MEGAHIT* +++++++++ An ultra-fast single-node solution for large and complex metagenomics assembly via succinct de Bruijn graph *homepage*: https://github.com/voutcn/megahit ========= ================== ============================== version versionsuffix toolchain ========= ================== ============================== ``1.1.2`` ``-Python-2.7.14`` ``foss/2018a`` ``1.1.3`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a`` ``1.1.3`` ``-Python-3.6.3`` ``foss/2017b`` ``1.1.4`` ``-Python-2.7.15`` ``foss/2018b`` ``1.1.4`` ``-Python-3.6.6`` ``foss/2018b`` ``1.2.8`` ``GCCcore/8.2.0`` ========= ================== ============================== .. _list_software_Meld_386: *Meld* ++++++ Meld is a visual diff and merge tool targeted at developers. Meld helps you compare files, directories, and version controlled projects. It provides two- and three-way comparison of both files and directories, and has support for many popular version control systems. *homepage*: https://meldmerge.org/ ========== ================= ================= version versionsuffix toolchain ========== ================= ================= ``3.20.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================= ================= .. _list_software_MEME_292: *MEME* ++++++ The MEME Suite allows you to: * discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences, * search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN, * compare a motif to all motifs in a database of motifs, * associate motifs with Gene Ontology terms via their putative target genes, and * analyse motif enrichment using SpaMo or CentriMo. *homepage*: http://meme-suite.org ========= ============================== =============================== version versionsuffix toolchain ========= ============================== =============================== ``5.0.4`` ``-Perl-5.26.0-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``5.0.4`` ``-Perl-5.26.0-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ========= ============================== =============================== .. _list_software_memkind_741: *memkind* +++++++++ User Extensible Heap Manager built on top of jemalloc which enables control of memory characteristics and a partitioning of the heap between kinds of memory. *homepage*: http://memkind.github.io ========= ================= version toolchain ========= ================= ``1.5.0`` ``GCCcore/5.4.0`` ========= ================= .. _list_software_memory-profiler_1577: *memory-profiler* +++++++++++++++++ memory-profiler is a Python module for monitoring memory consumption of a process as well as line-by-line analysis of memory consumption for python programs. *homepage*: https://pypi.org/project/memory-profiler ========== =============================== version toolchain ========== =============================== ``0.55.0`` ``foss/2019a``, ``intel/2019a`` ========== =============================== .. _list_software_meRanTK_658: *meRanTK* +++++++++ meRanTK is a versatile high performance toolkit for complete analysis of methylated RNA data. *homepage*: http://www.icbi.at/index.html ========== ========== version toolchain ========== ========== ``1.1.1b`` ``system`` ========== ========== .. _list_software_MERCKX_458: *MERCKX* ++++++++ Multilingual Entity/Resource Combiner & Knowledge eXtractor *homepage*: https://github.com/madewild/MERCKX ============ ================== =============== version versionsuffix toolchain ============ ================== =============== ``20170330`` ``-Python-2.7.13`` ``intel/2017a`` ============ ================== =============== .. _list_software_Mercurial_932: *Mercurial* +++++++++++ Mercurial is a free, distributed source control management tool. It efficiently handles projects of any size and offers an easy and intuitive interface. *homepage*: http://mercurial.selenic.com/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``3.8.3`` ``-Python-2.7.11`` ``foss/2016a`` ========= ================== ============== .. _list_software_Mesa_390: *Mesa* ++++++ Mesa is an open-source implementation of the OpenGL specification - a system for rendering interactive 3D graphics. *homepage*: https://www.mesa3d.org/ ========== ==================================================================== version toolchain ========== ==================================================================== ``11.1.2`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``11.2.1`` ``foss/2016a``, ``intel/2016a`` ``12.0.2`` ``foss/2016b``, ``intel/2016b`` ``17.0.2`` ``foss/2017a``, ``intel/2017a`` ``17.2.4`` ``intel/2017b``, ``intelcuda/2017b`` ``17.2.5`` ``foss/2017b``, ``fosscuda/2017b`` ``17.3.6`` ``foss/2018a``, ``fosscuda/2018a``, ``intel/2018a``, ``iomkl/2018a`` ``18.1.1`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``19.0.1`` ``GCCcore/8.2.0`` ``19.1.7`` ``GCCcore/8.3.0`` ``19.2.1`` ``GCCcore/8.3.0`` ========== ==================================================================== .. _list_software_meshio_645: *meshio* ++++++++ meshio is a tool for reading/writing various mesh formats representing unstructured meshes *homepage*: https://github.com/nschloe/meshio ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.7.1`` ``-Python-2.7.12`` ``intel/2016b`` ``2.0.2`` ``-Python-2.7.14`` ``intel/2018a`` ``2.0.2`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================== =============== .. _list_software_Meson_514: *Meson* +++++++ Meson is a cross-platform build system designed to be both as fast and as user friendly as possible. *homepage*: https://mesonbuild.com ========== ================= ================================== version versionsuffix toolchain ========== ================= ================================== ``0.43.0`` ``-Python-3.6.3`` ``intel/2017b`` ``0.46.1`` ``-Python-3.6.4`` ``foss/2018a`` ``0.48.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``0.48.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``0.50.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``0.51.2`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========== ================= ================================== .. _list_software_Mesquite_845: *Mesquite* ++++++++++ Mesh-Quality Improvement Library *homepage*: https://software.sandia.gov/mesquite/ ========= ======================================================================================== version toolchain ========= ======================================================================================== ``2.3.0`` ``GCCcore/6.4.0``, ``GCCcore/8.3.0``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017a`` ========= ======================================================================================== .. _list_software_MetaBAT_606: *MetaBAT* +++++++++ An efficient tool for accurately reconstructing single genomes from complex microbial communities *homepage*: https://bitbucket.org/berkeleylab/metabat ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``2.12.1`` ``-Python-2.7.15`` ``foss/2018b`` ``2.14`` ``gompi/2019a`` ========== ================== =============== .. _list_software_MetaboAnalystR_1414: *MetaboAnalystR* ++++++++++++++++ MetaboAnalystR contains the R functions and libraries underlying the popular MetaboAnalyst web server, including > 500 functions for metabolomic data analysis, visualization, and functional interpretation. *homepage*: https://www.metaboanalyst.ca ================== ============= ============== version versionsuffix toolchain ================== ============= ============== ``2.0.1-20190827`` ``-R-3.6.0`` ``foss/2019a`` ================== ============= ============== .. _list_software_MetaGeneAnnotator_1724: *MetaGeneAnnotator* +++++++++++++++++++ MetaGeneAnnotator is a gene-finding program for prokaryote and phage. *homepage*: http://metagene.nig.ac.jp/ ============ ============= ========== version versionsuffix toolchain ============ ============= ========== ``20080819`` ``-x86-64`` ``system`` ============ ============= ========== .. _list_software_Metal_499: *Metal* +++++++ Metal - Meta Analysis Helper. The METAL software is designed to facilitate meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner. *homepage*: http://csg.sph.umich.edu/abecasis/Metal/ ============== ============== version toolchain ============== ============== ``2011-03-25`` ``foss/2016a`` ============== ============== .. _list_software_MetaPhlAn2_908: *MetaPhlAn2* ++++++++++++ MetaPhlAn is a computational tool for profiling the composition of microbial communities (Bacteria, Archaea, Eukaryotes and Viruses) from metagenomic shotgun sequencing data (i.e. not 16S) with species-level. With the newly added StrainPhlAn module, it is now possible to perform accurate strain-level microbial profiling. *homepage*: https://bitbucket.org/biobakery/metaphlan2/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.7.8`` ``-Python-2.7.12`` ``foss/2016b`` ``2.7.8`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================== ============== .. _list_software_metaWRAP_737: *metaWRAP* ++++++++++ MetaWRAP aims to be an easy-to-use metagenomic wrapper suite that accomplishes the core tasks of metagenomic analysis from start to finish: read quality control, assembly, visualization, taxonomic profiling, extracting draft genomes (binning), and functional annotation. *homepage*: https://github.com/bxlab/metaWRAP ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.2`` ``-Python-2.7.15`` ``foss/2018b`` ``1.2.2`` ``-Python-2.7.15`` ``foss/2019a`` ========= ================== ============== .. _list_software_Metaxa2_658: *Metaxa2* +++++++++ Metaxa2 -- Identifies Small Subunit (SSU) rRNAs and classifies them taxonomically *homepage*: https://microbiology.se/software/metaxa2/ ======= =============== version toolchain ======= =============== ``2.2`` ``gompi/2019a`` ======= =============== .. _list_software_MethylDackel_1207: *MethylDackel* ++++++++++++++ A (mostly) universal methylation extractor for BS-seq experiments. *homepage*: https://github.com/dpryan79/MethylDackel ========= ======================================== version toolchain ========= ======================================== ``0.4.0`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ========= ======================================== .. _list_software_methylpy_892: *methylpy* ++++++++++ Bisulfite sequencing data processing and differential methylation analysis. *homepage*: https://pypi.python.org/pypi/methylpy ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.1.9`` ``-Python-2.7.13`` ``foss/2017a`` ========= ================== ============== .. _list_software_METIS_386: *METIS* +++++++ METIS is a set of serial programs for partitioning graphs, partitioning finite element meshes, and producing fill reducing orderings for sparse matrices. The algorithms implemented in METIS are based on the multilevel recursive-bisection, multilevel k-way, and multi-constraint partitioning schemes. *homepage*: http://glaros.dtc.umn.edu/gkhome/metis/metis/overview ========= ============= =============================================================================================================================================================================================================== version versionsuffix toolchain ========= ============= =============================================================================================================================================================================================================== ``5.0.2`` ``gimkl/2.11.5`` ``5.1.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``5.1.0`` ``-32bitIDX`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ============= =============================================================================================================================================================================================================== .. _list_software_mhcflurry_988: *mhcflurry* +++++++++++ MHCflurry implements class I peptide/MHC binding affinity prediction. By default it supports 112 MHC alleles using ensembles of allele-specific models. Pan-allele predictors supporting virtually any MHC allele of known sequence are available for testing (see below). MHCflurry runs on Python 2.7 and 3.4+ using the keras neural network library. It exposes command-line and Python library interfaces. *homepage*: https://github.com/openvax/mhcflurry ========= ================= ================================== version versionsuffix toolchain ========= ================= ================================== ``1.2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ========= ================= ================================== .. _list_software_MiGEC_389: *MiGEC* +++++++ MIGEC is a software pipeline that facilitates processing and analysis of immune repertoire sequencing data generated using molecular barcoding technique *homepage*: https://milaboratory.com/software/migec/ ========= =================== ========== version versionsuffix toolchain ========= =================== ========== ``1.2.8`` ``-Java-1.8.0_162`` ``system`` ========= =================== ========== .. _list_software_MIGRATE-N_644: *MIGRATE-N* +++++++++++ Migrate estimates population parameters, effective population sizes and migration rates of n populations, using genetic data. It uses a coalescent theory approach taking into account history of mutations and uncertainty of the genealogy. *homepage*: http://popgen.sc.fsu.edu/Migrate/Migrate-n.html ========== ============== version toolchain ========== ============== ``4.2.8`` ``foss/2016a`` ``4.2.14`` ``foss/2018a`` ========== ============== .. _list_software_MINC_295: *MINC* ++++++ Medical Image NetCDF or MINC isn't netCDF. *homepage*: https://github.com/BIC-MNI/libminc ========== =============================================== version toolchain ========== =============================================== ``2.4.03`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` ========== =============================================== .. _list_software_Miniconda2_964: *Miniconda2* ++++++++++++ Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages. *homepage*: https://docs.conda.io/en/latest/miniconda.html ========== ========== version toolchain ========== ========== ``4.3.21`` ``system`` ``4.6.14`` ``system`` ``4.7.10`` ``system`` ========== ========== .. _list_software_Miniconda3_965: *Miniconda3* ++++++++++++ Miniconda is a free minimal installer for conda. It is a small, bootstrap version of Anaconda that includes only conda, Python, the packages they depend on, and a small number of other useful packages. *homepage*: https://docs.conda.io/en/latest/miniconda.html ========== ========== version toolchain ========== ========== ``4.4.10`` ``system`` ``4.5.12`` ``system`` ``4.6.14`` ``system`` ``4.7.10`` ``system`` ========== ========== .. _list_software_minieigen_949: *minieigen* +++++++++++ A small wrapper for core parts of EIgen, c++ library for linear algebra. *homepage*: https://launchpad.net/minieigen/ ========= =============================== =============================== version versionsuffix toolchain ========= =============================== =============================== ``0.5.3`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``0.5.3`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``0.5.3`` ``-Python-2.7.12-Boost-1.63.0`` ``intel/2016b`` ``0.5.4`` ``-Python-2.7.14`` ``intel/2018a`` ========= =============================== =============================== .. _list_software_Minimac4_754: *Minimac4* ++++++++++ Minimac4 is a latest version in the series of genotype imputation software - preceded by Minimac3 (2015), Minimac2 (2014), minimac (2012) and MaCH (2010). Minimac4 is a lower memory and more computationally efficient implementation of the original algorithms with comparable imputation quality. *homepage*: https://genome.sph.umich.edu/wiki/Minimac4 ========= ============== version toolchain ========= ============== ``1.0.0`` ``foss/2018a`` ========= ============== .. _list_software_minimap2_797: *minimap2* ++++++++++ Minimap2 is a fast sequence mapping and alignment program that can find overlaps between long noisy reads, or map long reads or their assemblies to a reference genome optionally with detailed alignment (i.e. CIGAR). At present, it works efficiently with query sequences from a few kilobases to ~100 megabases in length at an error rate ~15%. Minimap2 outputs in the PAF or the SAM format. On limited test data sets, minimap2 is over 20 times faster than most other long-read aligners. It will replace BWA-MEM for long reads and contig alignment. *homepage*: https://github.com/lh3/minimap2 ========== ==================== version toolchain ========== ==================== ``2.0rc1`` ``foss/2016b`` ``2.10`` ``foss/2018a`` ``2.11`` ``intel/2018a`` ``2.12`` ``foss/2018a`` ``2.13`` ``foss/2018b`` ``2.17`` ``GCC/8.2.0-2.31.1`` ========== ==================== .. _list_software_MinPath_689: *MinPath* +++++++++ MinPath (Minimal set of Pathways) is a parsimony approach for biological pathway reconstructions using protein family predictions, achieving a more conservative, yet more faithful, estimation of the biological pathways for a query dataset. *homepage*: http://omics.informatics.indiana.edu/MinPath ======= ================== =============================== version versionsuffix toolchain ======= ================== =============================== ``1.4`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ======= ================== =============================== .. _list_software_MIRA_297: *MIRA* ++++++ MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the latter at the moment only CCS and error-corrected CLR reads). *homepage*: https://sourceforge.net/projects/mira-assembler/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``4.0.2`` ``intel/2017b`` ``4.0.2`` ``-Python-2.7.11`` ``foss/2016a`` ``4.9.6`` ``intel/2017b`` ========= ================== =============== .. _list_software_miRDeep2_728: *miRDeep2* ++++++++++ miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs *homepage*: https://www.mdc-berlin.de/8551903/en/ =========== ================= =============== version versionsuffix toolchain =========== ================= =============== ``0.1.1`` ``-Python-3.6.6`` ``foss/2018b`` ``2.0.0.8`` ``intel/2016b`` =========== ================= =============== .. _list_software_MiXCR_419: *MiXCR* +++++++ MiXCR processes big immunome data from raw sequences to quantitated clonotypes *homepage*: https://milaboratory.com/software/mixcr/ ========= =================== ========== version versionsuffix toolchain ========= =================== ========== ``2.1.9`` ``-Java-1.8.0_162`` ``system`` ``3.0.3`` ``-Java-1.8`` ``system`` ========= =================== ========== .. _list_software_mkl-dnn_689: *mkl-dnn* +++++++++ Intel(R) Math Kernel Library for Deep Neural Networks (Intel(R) MKL-DNN) *homepage*: https://01.org/mkl-dnn ========== =============================== version toolchain ========== =============================== ``0.11`` ``intel/2017b`` ``0.13`` ``intel/2018a`` ``0.16`` ``foss/2018b``, ``intel/2018b`` ``0.17.2`` ``foss/2018a`` ========== =============================== .. _list_software_mkl-service_1122: *mkl-service* +++++++++++++ Python hooks for Intel(R) Math Kernel Library runtime control settings. *homepage*: https://github.com/IntelPython/mkl-service ========= =============== version toolchain ========= =============== ``2.0.2`` ``intel/2019a`` ========= =============== .. _list_software_MLC_220: *MLC* +++++ Intel Memory Latency Checker (Intel MLC) is a tool used to measure memory latencies and b/w, and how they change with increasing load on the system. *homepage*: https://software.intel.com/en-us/articles/intelr-memory-latency-checker ======= ========== version toolchain ======= ========== ``3.0`` ``system`` ======= ========== .. _list_software_Mmg_289: *Mmg* +++++ Mmg is an open source software for simplicial remeshing. It provides 3 applications and 4 libraries: the mmg2d application and the libmmg2d library: adaptation and optimization of a two-dimensional triangulation and generation of a triangulation from a set of points or from given boundary edges the mmgs application and the libmmgs library: adaptation and optimization of a surface triangulation and isovalue discretization the mmg3d application and the libmmg3d library: adaptation and optimization of a tetrahedral mesh and implicit domain meshing the libmmg library gathering the libmmg2d, libmmgs and libmmg3d libraries *homepage*: https://www.mmgtools.org/ ========= ============== version toolchain ========= ============== ``5.3.9`` ``foss/2017b`` ========= ============== .. _list_software_MMSEQ_387: *MMSEQ* +++++++ The MMSEQ package contains a collection of statistical tools for analysing RNA-seq expression data. *homepage*: https://github.com/eturro/mmseq ========= =================== ========== version versionsuffix toolchain ========= =================== ========== ``1.0.8`` ``-linux64-static`` ``system`` ========= =================== ========== .. _list_software_MMseqs2_648: *MMseqs2* +++++++++ MMseqs2: ultra fast and sensitive search and clustering suite *homepage*: https://mmseqs.com =========== =============== version toolchain =========== =============== ``1-c7a89`` ``foss/2016b`` ``5-9375b`` ``intel/2018a`` ``8-fac81`` ``intel/2018b`` =========== =============== .. _list_software_modred_635: *modred* ++++++++ Compute modal decompositions and reduced-order models, easily, efficiently, and in parallel. *homepage*: https://pypi.python.org/pypi/modred/ ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``2.0.2`` ``-Python-3.5.2`` ``foss/2016b`` ========= ================= ============== .. _list_software_Molcas_607: *Molcas* ++++++++ Molcas is an ab initio quantum chemistry software package developed by scientists to be used by scientists. The basic philosophy is is to be able to treat general electronic structures for molecules consisting of atoms from most of the periodic table. As such, the primary focus of the package is on multiconfigurational methods with applications typically connected to the treatment of highly degenerate states. *homepage*: http://www.molcas.org ================ ====================== ========== version versionsuffix toolchain ================ ====================== ========== ``8.0-15.06.18`` ``_CentOS_6.6_x86_64`` ``system`` ``8.2`` ``-centos-mkl-par`` ``system`` ``8.2`` ``-centos-par`` ``system`` ================ ====================== ========== .. _list_software_Molden_607: *Molden* ++++++++ Molden is a package for displaying Molecular Density from the Ab Initio packages GAMESS-UK, GAMESS-US and GAUSSIAN and the Semi-Empirical packages Mopac/Ampac *homepage*: https://www.cmbi.ru.nl/molden/ ======= ================= version toolchain ======= ================= ``5.6`` ``foss/2016a`` ``5.7`` ``intel/2016b`` ``5.8`` ``foss/2018a`` ``6.1`` ``GCCcore/8.2.0`` ======= ================= .. _list_software_Molekel_713: *Molekel* +++++++++ Molekel is an open-source multi-platform molecular visualization program. *homepage*: http://molekel.cscs.ch/ ========= ================= ========== version versionsuffix toolchain ========= ================= ========== ``5.4.0`` ``-Linux_x86_64`` ``system`` ========= ================= ========== .. _list_software_molmod_648: *molmod* ++++++++ MolMod is a Python library with many compoments that are useful to write molecular modeling programs. *homepage*: https://molmod.github.io/molmod/ ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``1.1`` ``-Python-2.7.11`` ``intel/2016a`` ``1.1`` ``-Python-2.7.12`` ``intel/2016b`` ``1.1`` ``-Python-2.7.13`` ``intel/2017a`` ``1.4.3`` ``-Python-2.7.14`` ``intel/2017b`` ``1.4.3`` ``-Python-3.6.3`` ``intel/2017b`` ``1.4.4`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``1.4.4`` ``-Python-2.7.15`` ``intel/2018b`` ``1.4.4`` ``-Python-3.7.2`` ``intel/2019a`` ``1.4.5`` ``-Python-3.7.4`` ``intel/2019b`` ========= ================== =============================== .. _list_software_Molpro_633: *Molpro* ++++++++ Molpro is a complete system of ab initio programs for molecular electronic structure calculations. *homepage*: https://www.molpro.net ============= ======================== ========== version versionsuffix toolchain ============= ======================== ========== ``2010.1.23`` ``.Linux_x86_64`` ``system`` ``2015.1.0`` ``.linux_x86_64_intel`` ``system`` ``2015.1.3`` ``.linux_x86_64_openmp`` ``system`` ``2015.1.10`` ``.linux_x86_64_openmp`` ``system`` ============= ======================== ========== .. _list_software_Mono_409: *Mono* ++++++ An open source, cross-platform, implementation of C# and the CLR that is binary compatible with Microsoft.NET. *homepage*: https://www.mono-project.com/ ============== =============================== version toolchain ============== =============================== ``2.10.6`` ``intel/2016b`` ``4.6.2.7`` ``intel/2016b``, ``system`` ``4.8.0.495`` ``intel/2017a`` ``5.4.1.6`` ``foss/2017b``, ``intel/2017b`` ``5.10.0.160`` ``foss/2018a`` ``5.18.1.0`` ``foss/2018a`` ``6.4.0.198`` ``foss/2018b`` ============== =============================== .. _list_software_mordecai_836: *mordecai* ++++++++++ mordecai is a full text geoparsing as a Python library. Extract the place names from a piece of text, resolve them to the correct place, and return their coordinates and structured geographic information. *homepage*: https://github.com/openeventdata/mordecai ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``2.0.1`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================= ============== .. _list_software_mosdepth_868: *mosdepth* ++++++++++ Fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing *homepage*: https://github.com/brentp/mosdepth ========= =============== version toolchain ========= =============== ``0.2.2`` ``intel/2018a`` ``0.2.3`` ``intel/2018a`` ``0.2.4`` ``foss/2018b`` ========= =============== .. _list_software_Mothur_639: *Mothur* ++++++++ Mothur is a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. *homepage*: https://www.mothur.org/ ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``1.39.5`` ``-Python-2.7.13`` ``intel/2017a`` ``1.41.0`` ``-Python-2.7.15`` ``foss/2018b`` ``1.43.0`` ``-Python-3.7.2`` ``foss/2019a`` ========== ================== =============== .. _list_software_motif_543: *motif* +++++++ Motif refers to both a graphical user interface (GUI) specification and the widget toolkit for building applications that follow that specification under the X Window System on Unix and other POSIX-compliant systems. It was the standard toolkit for the Common Desktop Environment and thus for Unix. *homepage*: http://motif.ics.com/ ========= ================================================================================ version toolchain ========= ================================================================================ ``2.3.5`` ``foss/2016a``, ``intel/2016a`` ``2.3.7`` ``intel/2017a`` ``2.3.8`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a`` ========= ================================================================================ .. _list_software_MotionCor2_972: *MotionCor2* ++++++++++++ MotionCor2 correct anisotropic image motion at the single pixel level across the whole frame, suitable for both single particle and tomographic images. Iterative, patch-based motion detection is combined with spatial and temporal constraints and dose weighting. Cite publication: Shawn Q. Zheng, Eugene Palovcak, Jean-Paul Armache, Yifan Cheng and David A. Agard (2016) Anisotropic Correction of Beam-induced Motion for Improved Single-particle Electron Cryo-microscopy, Nature Methods, submitted. BioArxiv: https://biorxiv.org/content/early/2016/07/04/061960 *homepage*: https://msg.ucsf.edu/ ========= ================= version toolchain ========= ================= ``1.2.6`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_MoviePy_713: *MoviePy* +++++++++ MoviePy (full documentation) is a Python library for video editing: cutting, concatenations, title insertions, video compositing (a.k.a. non-linear editing), video processing, and creation of custom effects. *homepage*: https://zulko.github.io/moviepy/ ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``1.0.1`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================= ============== .. _list_software_MPC_224: *MPC* +++++ Gnu Mpc is a C library for the arithmetic of complex numbers with arbitrarily high precision and correct rounding of the result. It extends the principles of the IEEE-754 standard for fixed precision real floating point numbers to complex numbers, providing well-defined semantics for every operation. At the same time, speed of operation at high precision is a major design goal. *homepage*: http://www.multiprecision.org/ ========= =============== =============================== version versionsuffix toolchain ========= =============== =============================== ``1.0.3`` ``intel/2017a`` ``1.0.3`` ``-MPFR-3.1.6`` ``foss/2017b``, ``intel/2017b`` ========= =============== =============================== .. _list_software_MPFR_309: *MPFR* ++++++ The MPFR library is a C library for multiple-precision floating-point computations with correct rounding. *homepage*: https://www.mpfr.org ========= ================================================================ version toolchain ========= ================================================================ ``2.4.2`` ``system`` ``3.1.4`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``3.1.5`` ``GCCcore/6.4.0``, ``intel/2017a`` ``3.1.6`` ``GCCcore/6.4.0`` ``4.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``4.0.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ================================================================ .. _list_software_mpi4py_611: *mpi4py* ++++++++ MPI for Python (mpi4py) provides bindings of the Message Passing Interface (MPI) standard for the Python programming language, allowing any Python program to exploit multiple processors. *homepage*: https://bitbucket.org/mpi4py/mpi4py ========= ================================= ================================ version versionsuffix toolchain ========= ================================= ================================ ``1.3.1`` ``-Python-2.7.11-timed-pingpong`` ``intel/2016a`` ``1.3.1`` ``-Python-2.7.12-timed-pingpong`` ``intel/2016b`` ``2.0.0`` ``-Python-2.7.12`` ``intel/2016b`` ``2.0.0`` ``-Python-2.7.13-timed-pingpong`` ``intel/2017a`` ``3.0.0`` ``-Python-2.7.14-timed-pingpong`` ``intel/2018a`` ``3.0.0`` ``-Python-3.6.3`` ``intel/2017b`` ``3.0.1`` ``-Python-3.6.6`` ``intel/2018b`` ``3.0.2`` ``-timed-pingpong`` ``gompi/2019a``, ``iimpi/2019a`` ========= ================================= ================================ .. _list_software_MPICH_369: *MPICH* +++++++ MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). *homepage*: http://www.mpich.org/ ========= ====================================== version toolchain ========= ====================================== ``3.0.4`` ``GCC/4.8.1`` ``3.2`` ``GCC/4.9.3-2.25``, ``GCC/7.2.0-2.29`` ``3.2.1`` ``GCC/7.2.0-2.29`` ========= ====================================== .. _list_software_MPICH2_419: *MPICH2* ++++++++ MPICH v3.x is an open source high-performance MPI 3.0 implementation. It does not support InfiniBand (use MVAPICH2 with InfiniBand devices). *homepage*: http://www.mpich.org/ ======= ============= version toolchain ======= ============= ``1.1`` ``GCC/4.8.1`` ======= ============= .. _list_software_mpifileutils_1303: *mpifileutils* ++++++++++++++ MPI-Based File Utilities For Distributed Systems *homepage*: https://hpc.github.io/mpifileutils/ ========= ================================ version toolchain ========= ================================ ``0.9.1`` ``gompi/2019a``, ``iimpi/2019a`` ========= ================================ .. _list_software_mpiP_406: *mpiP* ++++++ mpiP is a lightweight profiling library for MPI applications. Because it only collects statistical information about MPI functions, mpiP generates considerably less overhead and much less data than tracing tools. All the information captured by mpiP is task-local. It only uses communication during report generation, typically at the end of the experiment, to merge results from all of the tasks into one output file. *homepage*: http://mpip.sourceforge.net/ ========= =================================================== version toolchain ========= =================================================== ``3.4.1`` ``gompi/2019a``, ``iimpi/2019a``, ``iompi/2019.01`` ========= =================================================== .. _list_software_MPJ-Express_1022: *MPJ-Express* +++++++++++++ MPJ Express is an open source Java message passing library that allows application developers to write and execute parallel applications for multicore processors and compute clusters/clouds. *homepage*: http://mpj-express.org/ ======== ================== ============== version versionsuffix toolchain ======== ================== ============== ``0.44`` ``-Java-1.8.0_92`` ``foss/2016a`` ======== ================== ============== .. _list_software_mpmath_647: *mpmath* ++++++++ mpmath can be used as an arbitrary-precision substitute for Python's float/complex types and math/cmath modules, but also does much more advanced mathematics. Almost any calculation can be performed just as well at 10-digit or 1000-digit precision, with either real or complex numbers, and in many cases mpmath implements efficient algorithms that scale well for extremely high precision work. *homepage*: http://mpmath.org/ ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``0.19`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``1.0.0`` ``-Python-2.7.14`` ``intel/2018a`` ``1.0.0`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== =============================== .. _list_software_MrBayes_691: *MrBayes* +++++++++ MrBayes is a program for the Bayesian estimation of phylogeny. *homepage*: http://mrbayes.csit.fsu.edu ========= ============== version toolchain ========= ============== ``3.2.6`` ``foss/2016a`` ========= ============== .. _list_software_MRIcron_666: *MRIcron* +++++++++ MRIcron allows viewing of medical images. It includes tools to complement SPM and FSL. Native format is NIFTI but includes a conversion program (see dcm2nii) for converting DICOM images. Features layers, ROIs, and volume rendering. *homepage*: http://www.mccauslandcenter.sc.edu/mricro/mricron/ ================ ========== version toolchain ================ ========== ``1.0.20180614`` ``system`` ``20150601`` ``system`` ================ ========== .. _list_software_MRtrix_614: *MRtrix* ++++++++ MRtrix provides a set of tools to perform diffusion-weighted MR white-matter tractography in a manner robust to crossing fibres, using constrained spherical deconvolution (CSD) and probabilistic streamlines. *homepage*: http://www.brain.org.au/software/index.html#mrtrix =================== ================== =============== version versionsuffix toolchain =================== ================== =============== ``0.3.14`` ``-Python-2.7.11`` ``intel/2016a`` ``0.3.15`` ``-Python-2.7.12`` ``intel/2016b`` ``3.0-rc-20191217`` ``-Python-2.7.16`` ``foss/2019b`` ``3.0-rc-20191217`` ``-Python-3.7.4`` ``foss/2019b`` ``3.0_RC2`` ``-Python-2.7.13`` ``foss/2017a`` ``3.0_RC3`` ``-Python-2.7.14`` ``intel/2018a`` =================== ================== =============== .. _list_software_MSM_237: *MSM* +++++ Multimodal Surface Matching with Higher order Clique Reduction *homepage*: https://github.com/ecr05/MSM_HOCR ======= =============================== version toolchain ======= =============================== ``1.0`` ``foss/2017b``, ``intel/2017b`` ======= =============================== .. _list_software_MSPC_307: *MSPC* ++++++ Using combined evidence from replicates to evaluate ChIP-seq peaks *homepage*: https://genometric.github.io/MSPC/ ========= ========== version toolchain ========= ========== ``3.3.1`` ``system`` ========= ========== .. _list_software_msprime_765: *msprime* +++++++++ msprime is a coalescent simulator and library for processing tree-based genetic data. *homepage*: https://msprime.readthedocs.io ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``0.7.0`` ``-Python-3.7.2`` ``intel/2019a`` ========= ================= =============== .. _list_software_MTL4_289: *MTL4* ++++++ The Matrix Template Library 4 incorporates the most modern programming techniques to provide an easy and intuitive interface to users while enabling optimal performance. The natural mathematical notation in MTL4 empowers all engineers and scientists to implement their algorithms and models in minimal time. All technical aspects are encapsulated in the library. *homepage*: http://www.simunova.com/mtl4 ============ ========== version toolchain ============ ========== ``4.0.8878`` ``system`` ``4.0.9555`` ``system`` ============ ========== .. _list_software_MultiNest_933: *MultiNest* +++++++++++ MultiNest is a Bayesian inference tool which calculates the evidence and explores the parameter space which may contain multiple posterior modes and pronounced (curving) degeneracies in moderately high dimensions. *homepage*: https://ccpforge.cse.rl.ac.uk/gf/project/multinest/ ======== =============== version toolchain ======== =============== ``3.10`` ``intel/2016a`` ======== =============== .. _list_software_MultiQC_671: *MultiQC* +++++++++ Aggregate results from bioinformatics analyses across many samples into a single report. MultiQC searches a given directory for analysis logs and compiles a HTML report. It's a general use tool, perfect for summarising the output from numerous bioinformatics tools. *homepage*: http://multiqc.info ======= ================== =============================== version versionsuffix toolchain ======= ================== =============================== ``0.9`` ``-Python-2.7.12`` ``foss/2016b`` ``1.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.6`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.6`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.7`` ``-Python-2.7.15`` ``intel/2018b`` ``1.7`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ======= ================== =============================== .. _list_software_Multiwfn_854: *Multiwfn* ++++++++++ Multiwfn is an extremely powerful program for realizingi electronic wavefunction analysis, which is a key ingredient of quantum chemistry. Multiwfn is free, open-source, high-efficient, very user-friendly and flexible, it supports almost all of the most important wavefunction analysis methods. *homepage*: http://sobereva.com/multiwfn/ ========= =============== version toolchain ========= =============== ``3.4.1`` ``intel/2017b`` ``3.6`` ``intel/2019a`` ========= =============== .. _list_software_MUMmer_563: *MUMmer* ++++++++ MUMmer is a system for rapidly aligning entire genomes, whether in complete or draft form. AMOS makes use of it. *homepage*: http://mummer.sourceforge.net/ ============== ============== version toolchain ============== ============== ``3.23`` ``foss/2016b`` ``4.0.0beta2`` ``foss/2018b`` ============== ============== .. _list_software_MUMPS_402: *MUMPS* +++++++ A parallel sparse direct solver *homepage*: http://graal.ens-lyon.fr/MUMPS/ ========= ============== =============================== version versionsuffix toolchain ========= ============== =============================== ``5.1.2`` ``-metis`` ``foss/2017b`` ``5.2.1`` ``-metis`` ``foss/2019a``, ``intel/2019a`` ``5.2.1`` ``-metis-seq`` ``foss/2019a``, ``intel/2019a`` ========= ============== =============================== .. _list_software_muParser_847: *muParser* ++++++++++ muParser is an extensible high performance math expression parser library written in C++. It works by transforming a mathematical expression into bytecode and precalculating constant parts of the expression. *homepage*: http://beltoforion.de/article.php?a=muparser ========= ================= version toolchain ========= ================= ``2.2.5`` ``GCCcore/6.4.0`` ========= ================= .. _list_software_MuPeXI_536: *MuPeXI* ++++++++ MuPeXI: Mutant Peptide eXtractor and Informer. Given a list of somatic mutations (VCF file) as input, MuPeXI returns a table containing all mutated peptides (neo-peptides) of user-defined lengths, along with several pieces of information relevant for identifying which of these neo-peptides are likely to serve as neo-epitopes. *homepage*: https://github.com/ambj/MuPeXI ========= ============================== ============== version versionsuffix toolchain ========= ============================== ============== ``1.2.0`` ``-Perl-5.28.0-Python-2.7.15`` ``foss/2018b`` ========= ============================== ============== .. _list_software_MUSCLE_457: *MUSCLE* ++++++++ MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes-only a handful of command-line options are needed to perform common alignment tasks. *homepage*: http://drive5.com/muscle/ ============ =============== ================================================================================================================== version versionsuffix toolchain ============ =============== ================================================================================================================== ``3.8.31`` ``foss/2016a``, ``foss/2017b``, ``foss/2018a``, ``intel/2016a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ``3.8.31`` ``-i86linux64`` ``system`` ``3.8.1551`` ``GCC/8.2.0-2.31.1`` ============ =============== ================================================================================================================== .. _list_software_MuSiC_449: *MuSiC* +++++++ Multi-subject Single Cell deconvolution (MuSiC) is a deconvolution method that utilizes cross-subject scRNA-seq to estimate cell type proportions in bulk RNA-seq data. *homepage*: https://github.com/xuranw/MuSiC ========= ============= ============== version versionsuffix toolchain ========= ============= ============== ``1.6.2`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== .. _list_software_MuTect_594: *MuTect* ++++++++ MuTect is a method developed at the Broad Institute for the reliable and accurate identification of somatic point mutations in next generation sequencing data of cancer genomes. *homepage*: http://www.broadinstitute.org/cancer/cga/mutect ========= ================== ========== version versionsuffix toolchain ========= ================== ========== ``1.1.4`` ``-Java-1.7.0_76`` ``system`` ``1.1.4`` ``-Java-1.7.0_80`` ``system`` ``1.1.7`` ``-Java-1.7.0_80`` ``system`` ========= ================== ========== .. _list_software_mutil_555: *mutil* +++++++ Mutil is a set of standard utilities that have been parallelized to maximize performance on modern file systems. These currently include multi-threaded drop-in replacements for cp and md5sum from GNU coreutils, which have achieved 10/30x rates on one/many nodes. *homepage*: http://people.nas.nasa.gov/~kolano/projects/mutil.html =========== =============== version toolchain =========== =============== ``1.822.3`` ``intel/2016a`` =========== =============== .. _list_software_MVAPICH2_570: *MVAPICH2* ++++++++++ This is an MPI 3.0 implementation. It is based on MPICH2 and MVICH. *homepage*: http://mvapich.cse.ohio-state.edu/overview/mvapich2/ ========= ================== version toolchain ========= ================== ``2.0.1`` ``GCC/4.8.4`` ``2.1`` ``GCC/4.9.3-2.25`` ``2.2b`` ``GCC/4.9.3-2.25`` ========= ================== .. _list_software_MXNet_460: *MXNet* +++++++ Flexible and Efficient Library for Deep Learning *homepage*: http://mxnet.io/ ========= ========================== ============== version versionsuffix toolchain ========= ========================== ============== ``0.9.3`` ``-Python-2.7.12-R-3.3.3`` ``foss/2016b`` ========= ========================== ============== .. _list_software_mygene_645: *mygene* ++++++++ Python Client for MyGene.Info services. *homepage*: https://github.com/biothings/mygene.py ========= =============== version toolchain ========= =============== ``3.1.0`` ``intel/2019a`` ========= =============== .. _list_software_MyMediaLite_1076: *MyMediaLite* +++++++++++++ MyMediaLite is a lightweight, multi-purpose library of recommender system algorithms. *homepage*: http://www.ismll.uni-hildesheim.de/mymedialite/ ======== =============== version toolchain ======== =============== ``3.10`` ``intel/2016b`` ``3.11`` ``intel/2016b`` ``3.12`` ``intel/2017a`` ======== =============== .. _list_software_mympingpong_1205: *mympingpong* +++++++++++++ A mpi4py based random pair pingpong network stress test. *homepage*: https://github.com/hpcugent/mympingpong ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``0.7.0`` ``-Python-2.7.11`` ``intel/2016a`` ``0.7.1`` ``-Python-2.7.12`` ``intel/2016b`` ``0.8.0`` ``-Python-2.7.13`` ``intel/2017a`` ``0.8.0`` ``-Python-2.7.14`` ``intel/2018a`` ``0.8.0`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2019a`` ========= ================== =============================== .. _list_software_mypy_463: *mypy* ++++++ Optional static typing for Python *homepage*: http://www.mypy-lang.org/ ========= =============== version toolchain ========= =============== ``0.4.5`` ``intel/2016b`` ========= =============== .. _list_software_MySQL_438: *MySQL* +++++++ MySQL is one of the world's most widely used open-source relational database management system (RDBMS). *homepage*: http://www.mysql.com/ ========== =============== ================== version versionsuffix toolchain ========== =============== ================== ``5.6.26`` ``-clientonly`` ``GNU/4.9.3-2.25`` ``5.7.21`` ``-clientonly`` ``GCCcore/6.4.0`` ========== =============== ================== .. _list_software_MySQL-python_1157: *MySQL-python* ++++++++++++++ MySQL database connector for Python *homepage*: https://github.com/farcepest/MySQLdb1 ========= ================================== =============== version versionsuffix toolchain ========= ================================== =============== ``1.2.5`` ``-Python-2.7.11`` ``intel/2016a`` ``1.2.5`` ``-Python-2.7.11-MariaDB-10.1.14`` ``intel/2016a`` ========= ================================== =============== .. _list_software_mysqlclient_1205: *mysqlclient* +++++++++++++ Python interface to MySQL *homepage*: https://github.com/PyMySQL/mysqlclient-python ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``1.3.7`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ========= ================== =============================== .. _list_software_letter_n: *N* --- :ref:`list_software_NAG_214` - :ref:`list_software_NAGfor_541` - :ref:`list_software_NAMD_288` - :ref:`list_software_nanofilt_859` - :ref:`list_software_nanonet_755` - :ref:`list_software_nanopolish_1083` - :ref:`list_software_NASM_303` - :ref:`list_software_NBO_223` - :ref:`list_software_NCBI-Toolkit_1071` - :ref:`list_software_ncbi-vdb_773` - :ref:`list_software_NCCL_288` - :ref:`list_software_ncdf4_463` - :ref:`list_software_ncdu_426` - :ref:`list_software_NCIPLOT_537` - :ref:`list_software_NCL_221` - :ref:`list_software_ncl_317` - :ref:`list_software_NCO_224` - :ref:`list_software_ncompress_986` - :ref:`list_software_ncurses_771` - :ref:`list_software_ncview_652` - :ref:`list_software_nd2reader_887` - :ref:`list_software_ne_211` - :ref:`list_software_NEdit_468` - :ref:`list_software_Net-core_765` - :ref:`list_software_netCDF_532` - :ref:`list_software_netCDF-C++_730` - :ref:`list_software_netCDF-C++4_782` - :ref:`list_software_netCDF-Fortran_1309` - :ref:`list_software_netcdf4-python_1399` - :ref:`list_software_netloc_645` - :ref:`list_software_NetLogo_696` - :ref:`list_software_netMHC_543` - :ref:`list_software_netMHCIIpan_1008` - :ref:`list_software_netMHCpan_862` - :ref:`list_software_NetPIPE_597` - :ref:`list_software_nettle_652` - :ref:`list_software_networkx_898` - :ref:`list_software_NeuroKit_817` - :ref:`list_software_NEURON_471` - :ref:`list_software_Nextflow_855` - :ref:`list_software_NextGenMap_983` - :ref:`list_software_NFFT_302` - :ref:`list_software_nglview_764` - :ref:`list_software_NGS_232` - :ref:`list_software_NGS-Python_919` - :ref:`list_software_NGSadmix_763` - :ref:`list_software_NiBabel_653` - :ref:`list_software_NIfTI_410` - :ref:`list_software_Nilearn_713` - :ref:`list_software_Nim_292` - :ref:`list_software_NIMBLE_439` - :ref:`list_software_Ninja_496` - :ref:`list_software_Nipype_629` - :ref:`list_software_NLopt_493` - :ref:`list_software_NLTK_313` - :ref:`list_software_Node-RED_654` - :ref:`list_software_nodejs_643` - :ref:`list_software_Normaliz_844` - :ref:`list_software_nose-parameterized_1871` - :ref:`list_software_novoalign_973` - :ref:`list_software_NOVOPlasty_959` - :ref:`list_software_npstat_666` - :ref:`list_software_NRGLjubljana_1146` - :ref:`list_software_NSPR_323` - :ref:`list_software_NSS_244` - :ref:`list_software_numactl_756` - :ref:`list_software_numba_531` - :ref:`list_software_numexpr_783` - :ref:`list_software_numpy_569` - :ref:`list_software_nvtop_567` - :ref:`list_software_NWChem_546` - :ref:`list_software_NxTrim_610` .. _list_software_NAG_214: *NAG* +++++ The worlds largest collection of robust, documented, tested and maintained numerical algorithms. *homepage*: http://www.nag.co.uk ======= ================================== version toolchain ======= ================================== ``24`` ``PGI/17.4-GCC-6.4.0-2.28`` ``26`` ``GCCcore/6.4.0``, ``intel/2018a`` ======= ================================== .. _list_software_NAGfor_541: *NAGfor* ++++++++ The checking compiler for improved code portability and detailed error reporting. *homepage*: http://www.nag.co.uk ========== ========== version toolchain ========== ========== ``6.2.14`` ``system`` ========== ========== .. _list_software_NAMD_288: *NAMD* ++++++ NAMD is a parallel molecular dynamics code designed for high-performance simulation of large biomolecular systems. *homepage*: http://www.ks.uiuc.edu/Research/namd/ ======== ============= ================================================================ version versionsuffix toolchain ======== ============= ================================================================ ``2.11`` ``-mpi`` ``intel/2016a`` ``2.12`` ``-mpi`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``2.13`` ``fosscuda/2018b`` ``2.13`` ``-mpi`` ``foss/2018b``, ``intel/2018b`` ======== ============= ================================================================ .. _list_software_nanofilt_859: *nanofilt* ++++++++++ Filtering and trimming of long read sequencing data. *homepage*: https://github.com/wdecoster/nanofilt ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``2.5.0`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== .. _list_software_nanonet_755: *nanonet* +++++++++ Nanonet provides recurrent neural network basecalling for Oxford Nanopore MinION data. *homepage*: https://github.com/nanoporetech/nanonet ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``2.0.0`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== .. _list_software_nanopolish_1083: *nanopolish* ++++++++++++ Software package for signal-level analysis of Oxford Nanopore sequencing data. *homepage*: https://github.com/jts/nanopolish ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``0.9.2`` ``intel/2018a`` ``0.10.2`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ========== ================== =============================== .. _list_software_NASM_303: *NASM* ++++++ NASM: General-purpose x86 assembler *homepage*: https://www.nasm.us/ =========== ==================================================================================== version toolchain =========== ==================================================================================== ``2.11.08`` ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a`` ``2.12.01`` ``foss/2016a``, ``intel/2016a`` ``2.12.02`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b``, ``intel/2017a``, ``system`` ``2.13.01`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``2.13.03`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.14.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` =========== ==================================================================================== .. _list_software_NBO_223: *NBO* +++++ The Natural Bond Orbital (NBO) program is a discovery tool for chemical insights from complex wavefunctions. *homepage*: http://nbo.chem.wisc.edu/ ======= =============== version toolchain ======= =============== ``1.1`` ``intel/2016a`` ``7.0`` ``intel/2017b`` ======= =============== .. _list_software_NCBI-Toolkit_1071: *NCBI-Toolkit* ++++++++++++++ The NCBI Toolkit is a collection of utilities developed for the production and distribution of GenBank, Entrez, BLAST, and related services by the National Center for Biotechnology Information. *homepage*: http://ncbi.github.io/cxx-toolkit/ ========== =============== version toolchain ========== =============== ``18.0.0`` ``intel/2017a`` ========== =============== .. _list_software_ncbi-vdb_773: *ncbi-vdb* ++++++++++ The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. *homepage*: https://github.com/ncbi/ncbi-vdb =========== ================================================ version toolchain =========== ================================================ ``2.5.8-1`` ``foss/2016b``, ``intel/2016a`` ``2.7.0`` ``foss/2016b`` ``2.8.2`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``2.9.1-1`` ``foss/2018a``, ``intel/2018a`` ``2.9.3`` ``foss/2018b`` =========== ================================================ .. _list_software_NCCL_288: *NCCL* ++++++ The NVIDIA Collective Communications Library (NCCL) implements multi-GPU and multi-node collective communication primitives that are performance optimized for NVIDIA GPUs. *homepage*: https://developer.nvidia.com/nccl ========== =================== ================== version versionsuffix toolchain ========== =================== ================== ``2.1.4`` ``-CUDA-9.0.176`` ``system`` ``2.2.13`` ``-CUDA-9.2.148.1`` ``system`` ``2.3.7`` ``fosscuda/2018b`` ``2.4.2`` ``gcccuda/2019a`` ``2.4.8`` ``gcccuda/2019b`` ========== =================== ================== .. _list_software_ncdf4_463: *ncdf4* +++++++ ncdf4: Interface to Unidata netCDF (version 4 or earlier) format data files *homepage*: https://cran.r-project.org/web/packages/ncdf4 ========== ============= =============================== version versionsuffix toolchain ========== ============= =============================== ``1.16`` ``-R-3.4.0`` ``intel/2017a`` ``1.16`` ``-R-3.4.3`` ``intel/2017b`` ``1.16`` ``-R-3.4.4`` ``intel/2018a`` ``1.16.1`` ``-R-3.5.1`` ``foss/2018b``, ``intel/2018b`` ``1.16.1`` ``-R-3.6.0`` ``foss/2019a`` ========== ============= =============================== .. _list_software_ncdu_426: *ncdu* ++++++ Ncdu is a disk usage analyzer with an ncurses interface. It is designed to find space hogs on a remote server where you don't have an entire graphical setup available, but it is a useful tool even on regular desktop systems. Ncdu aims to be fast, simple and easy to use, and should be able to run in any minimal POSIX-like environment with ncurses installed. *homepage*: https://dev.yorhel.nl/ncdu ======== ================= version toolchain ======== ================= ``1.13`` ``GCCcore/7.3.0`` ``1.14`` ``GCCcore/7.3.0`` ======== ================= .. _list_software_NCIPLOT_537: *NCIPLOT* +++++++++ NCIPLOT is a program for revealing non covalent interactions based on the reduced density gradient. *homepage*: https://www.lct.jussieu.fr/pagesperso/contrera/index-nci.html ================ ======================= version toolchain ================ ======================= ``4.0-20190718`` ``iccifort/2019.5.281`` ================ ======================= .. _list_software_NCL_221: *NCL* +++++ NCL is an interpreted language designed specifically for scientific data analysis and visualization. *homepage*: https://www.ncl.ucar.edu ========= ================================================= version toolchain ========= ================================================= ``6.4.0`` ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``6.5.0`` ``intel/2018a`` ``6.6.2`` ``foss/2018b``, ``intel/2018b``, ``intel/2019b`` ========= ================================================= .. _list_software_ncl_317: *ncl* +++++ The NEXUS Class Library is a C++ library for parsing NEXUS files. *homepage*: http://ncl.sourceforge.net/ ========== ==================== version toolchain ========== ==================== ``2.1.18`` ``GCC/8.2.0-2.31.1`` ========== ==================== .. _list_software_NCO_224: *NCO* +++++ manipulates and analyzes data stored in netCDF-accessible formats, including DAP, HDF4, and HDF5 *homepage*: http://nco.sourceforge.net ========= =============================== version toolchain ========= =============================== ``4.6.0`` ``foss/2016a`` ``4.6.6`` ``intel/2017a`` ``4.7.0`` ``intel/2017b`` ``4.7.1`` ``intel/2017b`` ``4.7.4`` ``foss/2017b`` ``4.7.6`` ``intel/2018a`` ``4.7.9`` ``foss/2018b``, ``intel/2018b`` ``4.8.1`` ``foss/2019a`` ========= =============================== .. _list_software_ncompress_986: *ncompress* +++++++++++ Compress is a fast, simple LZW file compressor. Compress does not have the highest compression rate, but it is one of the fastest programs to compress data. Compress is the defacto standard in the UNIX community for compressing files. *homepage*: http://ncompress.sourceforge.net/ =========== ================= version toolchain =========== ================= ``4.2.4.4`` ``GCCcore/6.4.0`` =========== ================= .. _list_software_ncurses_771: *ncurses* +++++++++ The Ncurses (new curses) library is a free software emulation of curses in System V Release 4.0, and more. It uses Terminfo format, supports pads and color and multiple highlights and forms characters and function-key mapping, and has all the other SYSV-curses enhancements over BSD Curses. *homepage*: http://www.gnu.org/software/ncurses/ ======= ============================================================================================================================================================================================================================================================================================================================================================================= version toolchain ======= ============================================================================================================================================================================================================================================================================================================================================================================= ``5.9`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25``, ``gimkl/2.11.5``, ``system`` ``6.0`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``6.1`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``system`` ======= ============================================================================================================================================================================================================================================================================================================================================================================= .. _list_software_ncview_652: *ncview* ++++++++ Ncview is a visual browser for netCDF format files. Typically you would use ncview to get a quick and easy, push-button look at your netCDF files. You can view simple movies of the data, view along various dimensions, take a look at the actual data values, change color maps, invert the data, etc. *homepage*: http://meteora.ucsd.edu/~pierce/ncview_home_page.html ========= ====================================================================================================================================================== version toolchain ========= ====================================================================================================================================================== ``2.1.7`` ``foss/2017b``, ``gompi/2019a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intel/2019b``, ``iomkl/2018b`` ========= ====================================================================================================================================================== .. _list_software_nd2reader_887: *nd2reader* +++++++++++ nd2reader is a pure-Python package that reads images produced by NIS Elements 4.0+. *homepage*: http://www.lighthacking.nl/nd2reader/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``3.0.6`` ``-Python-2.7.14`` ``intel/2017b`` ========= ================== =============== .. _list_software_ne_211: *ne* ++++ ne is a free (GPL'd) text editor based on the POSIX standard that runs (we hope) on almost any UN*X machine. ne is easy to use for the beginner, but powerful and fully configurable for the wizard, and most sparing in its resource usage. *homepage*: http://ne.di.unimi.it/ ========= =============== version toolchain ========= =============== ``3.0.1`` ``gimkl/2017a`` ========= =============== .. _list_software_NEdit_468: *NEdit* +++++++ NEdit is a multi-purpose text editor for the X Window System, which combines a standard, easy to use, graphical user interface with the thorough functionality and stability required by users who edit text eight hours a day. *homepage*: http://www.nedit.org ======= ============== ========== version versionsuffix toolchain ======= ============== ========== ``5.5`` ``-Linux-x86`` ``system`` ======= ============== ========== .. _list_software_Net-core_765: *Net-core* ++++++++++ .NET Core is a free and open-source managed computer software framework for the Windows, Linux, and macOS operating systems .NET Core fully supports C# and F# and partially supports Visual Basic *homepage*: https://dotnet.microsoft.com/ ========= ========== version toolchain ========= ========== ``2.1.8`` ``system`` ``2.2.5`` ``system`` ``3.0.0`` ``system`` ========= ========== .. _list_software_netCDF_532: *netCDF* ++++++++ NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. *homepage*: https://www.unidata.ucar.edu/software/netcdf/ =========== ================ ========================================================================================================================== version versionsuffix toolchain =========== ================ ========================================================================================================================== ``4.3.3.1`` ``foss/2016a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a`` ``4.4.0`` ``foss/2016a``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``4.4.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``4.4.1.1`` ``foss/2016b``, ``foss/2017b``, ``fosscuda/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` ``4.4.1.1`` ``-HDF5-1.10.1`` ``foss/2017a``, ``intel/2017a`` ``4.4.1.1`` ``-HDF5-1.8.18`` ``intel/2017a`` ``4.4.1.1`` ``-HDF5-1.8.19`` ``foss/2017a``, ``foss/2017b``, ``intel/2017b`` ``4.5.0`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01`` ``4.6.0`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` ``4.6.1`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``4.6.2`` ``gompi/2019a``, ``iimpi/2019a`` ``4.7.1`` ``gompi/2019b``, ``gompic/2019b``, ``iimpi/2019b``, ``iimpic/2019b`` =========== ================ ========================================================================================================================== .. _list_software_netCDF-C++_730: *netCDF-C++* ++++++++++++ NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. *homepage*: http://www.unidata.ucar.edu/software/netcdf/ ======= ============== version toolchain ======= ============== ``4.2`` ``foss/2016a`` ======= ============== .. _list_software_netCDF-C++4_782: *netCDF-C++4* +++++++++++++ NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. *homepage*: https://www.unidata.ucar.edu/software/netcdf/ ========= ================ ====================================================================================================================================================== version versionsuffix toolchain ========= ================ ====================================================================================================================================================== ``4.3.0`` ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``4.3.0`` ``-HDF5-1.8.18`` ``intel/2017a`` ``4.3.0`` ``-HDF5-1.8.19`` ``intel/2017b`` ``4.3.1`` ``iimpi/2019b`` ========= ================ ====================================================================================================================================================== .. _list_software_netCDF-Fortran_1309: *netCDF-Fortran* ++++++++++++++++ NetCDF (network Common Data Form) is a set of software libraries and machine-independent data formats that support the creation, access, and sharing of array-oriented scientific data. *homepage*: https://www.unidata.ucar.edu/software/netcdf/ ========= ================ ==================================================================================================================================================================================================================================================================================================================================== version versionsuffix toolchain ========= ================ ==================================================================================================================================================================================================================================================================================================================================== ``4.4.1`` ``foss/2016b``, ``intel/2016b`` ``4.4.2`` ``intel/2016.02-GCC-4.9`` ``4.4.3`` ``foss/2016a``, ``intel/2016a`` ``4.4.4`` ``PGI/18.4-GCC-6.4.0-2.28``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2017b``, ``fosscuda/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``intelcuda/2017b``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``iomkl/2018b`` ``4.4.4`` ``-HDF5-1.8.18`` ``intel/2017a`` ``4.4.4`` ``-HDF5-1.8.19`` ``foss/2017b``, ``intel/2017b`` ``4.4.5`` ``gompi/2019a``, ``iimpi/2019a`` ``4.5.2`` ``iimpi/2019b`` ========= ================ ==================================================================================================================================================================================================================================================================================================================================== .. _list_software_netcdf4-python_1399: *netcdf4-python* ++++++++++++++++ Python/numpy interface to netCDF. *homepage*: https://unidata.github.io/netcdf4-python/ ========= ============================= =============== version versionsuffix toolchain ========= ============================= =============== ``1.2.9`` ``-Python-2.7.13`` ``intel/2017a`` ``1.3.1`` ``-Python-3.6.3`` ``intel/2017b`` ``1.3.1`` ``-Python-3.6.3-HDF5-1.8.19`` ``intel/2017b`` ``1.4.0`` ``-Python-3.6.2-HDF5-1.8.19`` ``foss/2017b`` ``1.4.0`` ``-Python-3.6.4`` ``intel/2018a`` ``1.4.1`` ``-Python-2.7.15`` ``intel/2018b`` ``1.4.1`` ``-Python-3.6.6`` ``intel/2018b`` ``1.4.2`` ``-Python-3.6.4`` ``foss/2018a`` ``1.4.3`` ``-Python-3.6.6`` ``foss/2018b`` ``1.5.2`` ``intel/2019a`` ========= ============================= =============== .. _list_software_netloc_645: *netloc* ++++++++ The Portable Network Locality (netloc) software package provides network topology discovery tools, and an abstract representation of those networks topologies for a range of network types and configurations. It is provided as a companion to the Portable Hardware Locality (hwloc) package. *homepage*: http://www.open-mpi.org/software/netloc ======= ============= version toolchain ======= ============= ``0.5`` ``GCC/4.8.3`` ======= ============= .. _list_software_NetLogo_696: *NetLogo* +++++++++ NetLogo is a multi-agent programmable modeling environment. It is used by tens of thousands of students, teachers and researchers worldwide. It also powers HubNet participatory simulations. It is authored by Uri Wilensky and developed at the CCL. *homepage*: http://ccl.northwestern.edu/netlogo/ ========= ============= ========== version versionsuffix toolchain ========= ============= ========== ``5.3.1`` ``-64`` ``system`` ``6.0.4`` ``-64`` ``system`` ========= ============= ========== .. _list_software_netMHC_543: *netMHC* ++++++++ NetMHC 4.0 software predicts binding of peptides to a number of different HLA alleles using artificial neural networks (ANN). *homepage*: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHC ======== ========== version toolchain ======== ========== ``4.0a`` ``system`` ======== ========== .. _list_software_netMHCIIpan_1008: *netMHCIIpan* +++++++++++++ The NetMHCIIpan software predicts binding of peptides to MHC class II molecules. The predictions are available for the three human MHC class II isotypes HLA-DR, HLA-DP and HLA-DQ, as well as mouse molecules (H-2). *homepage*: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCIIpan ======= ================= version toolchain ======= ================= ``3.2`` ``GCCcore/7.3.0`` ======= ================= .. _list_software_netMHCpan_862: *netMHCpan* +++++++++++ The NetMHCpan software predicts binding of peptides to any known MHC molecule using artificial neural networks (ANNs). *homepage*: http://www.cbs.dtu.dk/cgi-bin/nph-sw_request?netMHCpan ======== ========== version toolchain ======== ========== ``4.0a`` ``system`` ======== ========== .. _list_software_NetPIPE_597: *NetPIPE* +++++++++ NetPIPE is a protocol independent communication performance benchmark that visually represents the network performance under a variety of conditions. *homepage*: http://netpipe.cs.ksu.edu/ ======= =============== version toolchain ======= =============== ``5.1`` ``intel/2018a`` ======= =============== .. _list_software_nettle_652: *nettle* ++++++++ Nettle is a cryptographic library that is designed to fit easily in more or less any context: In crypto toolkits for object-oriented languages (C++, Python, Pike, ...), in applications like LSH or GNUPG, or even in kernel space. *homepage*: http://www.lysator.liu.se/~nisse/nettle/ ========= =========================================================================================================================================== version toolchain ========= =========================================================================================================================================== ``3.1.1`` ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` ``3.2`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` ``3.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``intel/2017a`` ``3.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018a`` ``3.4.1`` ``GCCcore/8.2.0`` ``3.5.1`` ``GCCcore/8.3.0`` ========= =========================================================================================================================================== .. _list_software_networkx_898: *networkx* ++++++++++ NetworkX is a Python package for the creation, manipulation, and study of the structure, dynamics, and functions of complex networks. *homepage*: https://pypi.python.org/pypi/networkx ======== ================== =============================== version versionsuffix toolchain ======== ================== =============================== ``1.1`` ``-Python-2.7.12`` ``intel/2016b`` ``1.11`` ``-Python-2.7.11`` ``foss/2016a`` ``1.11`` ``-Python-2.7.14`` ``intel/2017b`` ``1.11`` ``-Python-3.5.1`` ``foss/2016a`` ``2.0`` ``-Python-2.7.14`` ``intel/2017b`` ``2.1`` ``-Python-2.7.14`` ``intel/2017b`` ``2.2`` ``-Python-2.7.15`` ``intel/2018b`` ``2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``2.3`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``2.4`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``2.4`` ``-Python-3.7.4`` ``foss/2019b`` ======== ================== =============================== .. _list_software_NeuroKit_817: *NeuroKit* ++++++++++ NeuroKit is a Python module that provides high-level integrative functions with good and flexible defaults, allowing users to focus on what’s important. *homepage*: https://neurokit.readthedocs.io ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``0.2.7`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== .. _list_software_NEURON_471: *NEURON* ++++++++ Empirically-based simulations of neurons and networks of neurons. *homepage*: http://www.neuron.yale.edu/neuron ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``7.4`` ``intel/2016b`` ``7.6.5`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============== .. _list_software_Nextflow_855: *Nextflow* ++++++++++ Nextflow is a reactive workflow framework and a programming DSL that eases writing computational pipelines with complex data *homepage*: https://www.nextflow.io/ =========== ========== version toolchain =========== ========== ``19.04.0`` ``system`` ``19.07.0`` ``system`` =========== ========== .. _list_software_NextGenMap_983: *NextGenMap* ++++++++++++ NextGenMap is a flexible highly sensitive short read mapping tool that handles much higher mismatch rates than comparable algorithms while still outperforming them in terms of runtime. *homepage*: http://cibiv.github.io/NextGenMap/ ========= ============== version toolchain ========= ============== ``0.5.5`` ``foss/2016b`` ========= ============== .. _list_software_NFFT_302: *NFFT* ++++++ The NFFT (nonequispaced fast Fourier transform or nonuniform fast Fourier transform) is a C subroutine library for computing the nonequispaced discrete Fourier transform (NDFT) and its generalisations in one or more dimensions, of arbitrary input size, and of complex data. *homepage*: https://www-user.tu-chemnitz.de/~potts/nfft/ ========= ============================== version toolchain ========= ============================== ``3.5.1`` ``foss/2018b``, ``foss/2019a`` ========= ============================== .. _list_software_nglview_764: *nglview* +++++++++ IPython widget to interactively view molecular structures and trajectories. *homepage*: https://github.com/arose/nglview ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``2.7.0`` ``-Python-3.7.2`` ``intel/2019a`` ========= ================= =============== .. _list_software_NGS_232: *NGS* +++++ NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. *homepage*: https://github.com/ncbi/ngs ========== =================== ================================== version versionsuffix toolchain ========== =================== ================================== ``1.2.3`` ``foss/2016b``, ``intel/2016a`` ``1.2.5`` ``foss/2016b`` ``1.3.0`` ``GCCcore/6.4.0``, ``intel/2017a`` ``2.9.1`` ``-Java-1.8.0_162`` ``foss/2018a``, ``intel/2018a`` ``2.9.3`` ``-Java-1.8`` ``foss/2018b`` ``2.10.0`` ``-Java-1.8`` ``GCCcore/8.2.0`` ``2.10.0`` ``-Java-11`` ``GCCcore/8.2.0`` ========== =================== ================================== .. _list_software_NGS-Python_919: *NGS-Python* ++++++++++++ NGS is a new, domain-specific API for accessing reads, alignments and pileups produced from Next Generation Sequencing. *homepage*: https://github.com/ncbi/ngs ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.2.3`` ``-Python-2.7.11`` ``intel/2016a`` ========= ================== =============== .. _list_software_NGSadmix_763: *NGSadmix* ++++++++++ NGSadmix is a tool for finding admixture proportions from NGS data, based on genotype likelihoods. *homepage*: http://www.popgen.dk/software/index.php/NgsAdmix ======= ================== version toolchain ======= ================== ``32`` ``GCC/7.3.0-2.30`` ======= ================== .. _list_software_NiBabel_653: *NiBabel* +++++++++ NiBabel provides read/write access to some common medical and neuroimaging file formats, including: ANALYZE (plain, SPM99, SPM2 and later), GIFTI, NIfTI1, NIfTI2, MINC1, MINC2, MGH and ECAT as well as Philips PAR/REC. We can read and write Freesurfer geometry, and read Freesurfer morphometry and annotation files. There is some very limited support for DICOM. NiBabel is the successor of PyNIfTI. *homepage*: https://nipy.github.io/nibabel ========= ================================= =============================== version versionsuffix toolchain ========= ================================= =============================== ``2.0.2`` ``-Python-2.7.11`` ``intel/2016a`` ``2.0.2`` ``-Python-2.7.11-freetype-2.6.3`` ``intel/2016a`` ``2.1.0`` ``-Python-2.7.13`` ``intel/2017a`` ``2.2.1`` ``-Python-3.6.4`` ``intel/2018a`` ``2.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``2.3.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``2.3.0`` ``-Python-3.6.6`` ``foss/2018b`` ``2.4.0`` ``foss/2019a``, ``intel/2019a`` ``2.5.1`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================================= =============================== .. _list_software_NIfTI_410: *NIfTI* +++++++ Niftilib is a set of i/o libraries for reading and writing files in the nifti-1 data format. *homepage*: http://niftilib.sourceforge.net/ ========= ================= version toolchain ========= ================= ``2.0.0`` ``GCCcore/6.4.0`` ========= ================= .. _list_software_Nilearn_713: *Nilearn* +++++++++ Nilearn is a Python module for fast and easy statistical learning on NeuroImaging data. *homepage*: http://nilearn.github.io/ ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``0.5.2`` ``foss/2019a``, ``intel/2019a`` ``0.5.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``0.5.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ========= ================== =============================== .. _list_software_Nim_292: *Nim* +++++ Nim is a systems and applications programming language. *homepage*: https://nim-lang.org/ ========== ================= version toolchain ========== ================= ``0.18.0`` ``GCCcore/6.4.0`` ``0.19.2`` ``GCCcore/7.3.0`` ``1.0.0`` ``GCCcore/8.3.0`` ========== ================= .. _list_software_NIMBLE_439: *NIMBLE* ++++++++ NIMBLE is a system for building and sharing analysis methods for statistical models, especially for hierarchical models and computationally-intensive methods. *homepage*: https://r-nimble.org ========= ============= ============== version versionsuffix toolchain ========= ============= ============== ``0.7.0`` ``-R-3.5.1`` ``foss/2018b`` ========= ============= ============== .. _list_software_Ninja_496: *Ninja* +++++++ Ninja is a small build system with a focus on speed. *homepage*: https://ninja-build.org/ ========= ==================================================================================== version toolchain ========= ==================================================================================== ``1.8.2`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2017b``, ``intel/2018a`` ``1.9.0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` ========= ==================================================================================== .. _list_software_Nipype_629: *Nipype* ++++++++ Nipype is a Python project that provides a uniform interface to existing neuroimaging software and facilitates interaction between these packages within a single workflow. *homepage*: http://nipy.org/nipype ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``1.0.2`` ``-Python-3.6.4`` ``intel/2018a`` ``1.1.3`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= =============== .. _list_software_NLopt_493: *NLopt* +++++++ NLopt is a free/open-source library for nonlinear optimization, providing a common interface for a number of different free optimization routines available online as well as original implementations of various other algorithms. *homepage*: http://ab-initio.mit.edu/wiki/index.php/NLopt ========= =================================================================================================================================================================================================================================================== version toolchain ========= =================================================================================================================================================================================================================================================== ``2.4.2`` ``GCC/5.4.0-2.26``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``iomkl/2018a`` ``2.6.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= =================================================================================================================================================================================================================================================== .. _list_software_NLTK_313: *NLTK* ++++++ NLTK is a leading platform for building Python programs to work with human language data. *homepage*: http://www.nltk.org/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``3.2.2`` ``-Python-2.7.13`` ``intel/2017a`` ``3.2.4`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== .. _list_software_Node-RED_654: *Node-RED* ++++++++++ Node-RED is a programming tool for wiring together hardware devices, APIs and online services in new and interesting ways. *homepage*: http://nodered.org ========== ============== version toolchain ========== ============== ``0.16.2`` ``foss/2017a`` ========== ============== .. _list_software_nodejs_643: *nodejs* ++++++++ Node.js is a platform built on Chrome's JavaScript runtime for easily building fast, scalable network applications. Node.js uses an event-driven, non-blocking I/O model that makes it lightweight and efficient, perfect for data-intensive real-time applications that run across distributed devices. *homepage*: http://nodejs.org =========== ================= version toolchain =========== ================= ``4.4.7`` ``foss/2016a`` ``6.10.3`` ``foss/2017a`` ``8.9.4`` ``foss/2017a`` ``10.15.1`` ``foss/2018b`` ``10.15.3`` ``GCCcore/8.2.0`` =========== ================= .. _list_software_Normaliz_844: *Normaliz* ++++++++++ Normaliz is an open source tool for computations in affine monoids, vector configurations, lattice polytopes, and rational cones. *homepage*: https://www.normaliz.uni-osnabrueck.de/ ========= =============== version toolchain ========= =============== ``3.6.3`` ``intel/2018b`` ========= =============== .. _list_software_nose-parameterized_1871: *nose-parameterized* ++++++++++++++++++++ Parameterized testing with any Python test framework. *homepage*: hmat://github.com/wolever/nose-parameterized ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.5.0`` ``-Python-2.7.11`` ``foss/2016a`` ``0.5.0`` ``-Python-3.5.1`` ``foss/2016a`` ``0.5.0`` ``-Python-3.5.2`` ``intel/2016b`` ``0.6.0`` ``-Python-3.6.1`` ``intel/2017a`` ========= ================== =============== .. _list_software_novoalign_973: *novoalign* +++++++++++ NovoCraft is a software bundle. NovoAlign: Market’s leading aligner with fully packed features designed for mapping of short reads onto a reference genome from Illumina, Ion Torrent, 454, and Color Spance NGS platforms. NovoAlignCS: Leading aligner packed with features designed to fully support reads from ABI SOLiD Color Space. NovoSort: Custom designed multi-threaded sort/merge tools for BAM files. NovoMethyl: It can analyse a set of alignments to identify methylated cytosine’s. WARNING! You can only use the sofware without a license (with some features disabled) if you are a non-profit organisation and use is for your own research or for use by students as part of their course. A license is required for use where these programs are part of a service where a third party is billed. *homepage*: http://www.novocraft.com/ =========== ============= ============== version versionsuffix toolchain =========== ============= ============== ``3.09.00`` ``system`` ``3.09.01`` ``-R-3.5.1`` ``foss/2018b`` =========== ============= ============== .. _list_software_NOVOPlasty_959: *NOVOPlasty* ++++++++++++ NOVOPlasty is a de novo assembler and heteroplasmy/variance caller for short circular genomes. *homepage*: https://github.com/ndierckx/NOVOPlasty ======= ================= version toolchain ======= ================= ``3.7`` ``GCCcore/8.3.0`` ======= ================= .. _list_software_npstat_666: *npstat* ++++++++ npstat implements some population genetics tests and estimators that can be applied to pooled sequences from Next Generation Sequencing experiments. *homepage*: https://code.google.com/archive/p/npstat/ ======== =============================== version toolchain ======== =============================== ``0.99`` ``foss/2016a``, ``intel/2016a`` ======== =============================== .. _list_software_NRGLjubljana_1146: *NRGLjubljana* ++++++++++++++ NRG Ljubljana is an efficient implementation of the numerical renormalization group (NRG) technique for solving quantum impurity problems that arise as simplified models of magnetic impurities and as effective models in the dynamical mean field theory (DMFT) approach to bulk correlated materials. *homepage*: http://nrgljubljana.ijs.si/ ============ ============== version toolchain ============ ============== ``2.4.3.23`` ``foss/2016b`` ============ ============== .. _list_software_NSPR_323: *NSPR* ++++++ Netscape Portable Runtime (NSPR) provides a platform-neutral API for system level and libc-like functions. *homepage*: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSPR ======== ==================================== version toolchain ======== ==================================== ``4.20`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``4.21`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ======== ==================================== .. _list_software_NSS_244: *NSS* +++++ Network Security Services (NSS) is a set of libraries designed to support cross-platform development of security-enabled client and server applications. *homepage*: https://developer.mozilla.org/en-US/docs/Mozilla/Projects/NSS ========== ==================================== version toolchain ========== ==================================== ``3.39`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``3.42.1`` ``GCCcore/8.2.0`` ``3.45`` ``GCCcore/8.3.0`` ========== ==================================== .. _list_software_numactl_756: *numactl* +++++++++ The numactl program allows you to run your application program on specific cpu's and memory nodes. It does this by supplying a NUMA memory policy to the operating system before running your program. The libnuma library provides convenient ways for you to add NUMA memory policies into your own program. *homepage*: http://oss.sgi.com/projects/libnuma/ ========== ============================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain ========== ============================================================================================================================================================================================================================================================================================================================================================================================================================================== ``2.0.9`` ``GCC/4.8.3`` ``2.0.10`` ``GCC/4.8.4``, ``GCC/4.9.2``, ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25`` ``2.0.11`` ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/5.2.0``, ``GCC/5.3.0-2.26``, ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``GCC/6.2.0-2.27``, ``GCC/6.3.0-2.27``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``iccifort/2016.3.210-GCC-4.9.3-2.25``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016a``, ``intel/2016b`` ``2.0.12`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``2.0.13`` ``GCCcore/9.2.0`` ========== ============================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_numba_531: *numba* +++++++ Numba is an Open Source NumPy-aware optimizing compiler for Python sponsored by Continuum Analytics, Inc. It uses the remarkable LLVM compiler infrastructure to compile Python syntax to machine code. *homepage*: https://numba.pydata.org/ ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``0.24.0`` ``-Python-2.7.11`` ``intel/2016a`` ``0.24.0`` ``-Python-3.5.1`` ``intel/2016a`` ``0.26.0`` ``-Python-2.7.11`` ``intel/2016a`` ``0.32.0`` ``-Python-2.7.13`` ``intel/2017a`` ``0.37.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` ``0.37.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``0.43.1`` ``intel/2019a`` ``0.46.0`` ``foss/2019a`` ========== ================== =============================== .. _list_software_numexpr_783: *numexpr* +++++++++ The numexpr package evaluates multiple-operator array expressions many times faster than NumPy can. It accepts the expression as a string, analyzes it, rewrites it more efficiently, and compiles it on the fly into code for its internal virtual machine (VM). Due to its integrated just-in-time (JIT) compiler, it does not require a compiler at runtime. *homepage*: https://numexpr.readthedocs.io ========= ================== ================================== version versionsuffix toolchain ========= ================== ================================== ``2.5.2`` ``-Python-2.7.11`` ``intel/2016a`` ``2.6.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``2.6.1`` ``-Python-3.5.2`` ``intel/2016b`` ``2.6.4`` ``-Python-2.7.13`` ``foss/2017a`` ``2.6.4`` ``-Python-2.7.14`` ``intel/2018a`` ``2.6.4`` ``-Python-3.5.1`` ``foss/2016a`` ``2.6.4`` ``-Python-3.6.1`` ``intel/2017a`` ``2.6.4`` ``-Python-3.6.3`` ``intel/2017b`` ``2.6.4`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``2.6.5`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.6.5`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``2.7.0`` ``intel/2019a`` ========= ================== ================================== .. _list_software_numpy_569: *numpy* +++++++ NumPy is the fundamental package for scientific computing with Python. It contains among other things: a powerful N-dimensional array object, sophisticated (broadcasting) functions, tools for integrating C/C++ and Fortran code, useful linear algebra, Fourier transform, and random number capabilities. Besides its obvious scientific uses, NumPy can also be used as an efficient multi-dimensional container of generic data. Arbitrary data-types can be defined. This allows NumPy to seamlessly and speedily integrate with a wide variety of databases. *homepage*: http://www.numpy.org ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``1.8.2`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``1.9.2`` ``-Python-2.7.12`` ``intel/2016b`` ``1.10.4`` ``-Python-2.7.11`` ``intel/2016a`` ``1.11.0`` ``-Python-2.7.11`` ``intel/2016a`` ``1.12.1`` ``-Python-3.5.2`` ``intel/2016b`` ``1.13.0`` ``-Python-2.7.13`` ``intel/2017a`` ``1.13.1`` ``-Python-3.6.1`` ``intel/2017a`` ========== ================== =============================== .. _list_software_nvtop_567: *nvtop* +++++++ htop-like GPU usage monitor *homepage*: https://github.com/Syllo/nvtop ========= ================== version toolchain ========= ================== ``1.0.0`` ``fosscuda/2018b`` ========= ================== .. _list_software_NWChem_546: *NWChem* ++++++++ NWChem aims to provide its users with computational chemistry tools that are scalable both in their ability to treat large scientific computational chemistry problems efficiently, and in their use of available parallel computing resources from high-performance parallel supercomputers to conventional workstation clusters. NWChem software can handle: biomolecules, nanostructures, and solid-state; from quantum to classical, and all combinations; Gaussian basis functions or plane-waves; scaling from one to thousands of processors; properties and relativity. *homepage*: http://www.nwchem-sw.org ===================== ============================================== ================================ version versionsuffix toolchain ===================== ============================================== ================================ ``6.6.revision27746`` ``-2015-10-20-Python-2.7.12`` ``iomkl/2017a`` ``6.6.revision27746`` ``-2015-10-20-patches-20170814-Python-2.7.13`` ``intel/2017a`` ``6.8.revision47`` ``-2017-12-14-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` ===================== ============================================== ================================ .. _list_software_NxTrim_610: *NxTrim* ++++++++ NxTrim is a software to remove Nextera Mate Pair junction adapters and categorise reads according to the orientation implied by the adapter location. *homepage*: https://github.com/sequencing/NxTrim ========= ============== version toolchain ========= ============== ``0.4.3`` ``foss/2018a`` ========= ============== .. _list_software_letter_o: *O* --- :ref:`list_software_Oases_507` - :ref:`list_software_OBITools_747` - :ref:`list_software_OCaml_460` - :ref:`list_software_Octave_610` - :ref:`list_software_OMA_221` - :ref:`list_software_OOMPA_380` - :ref:`list_software_OPARI2_429` - :ref:`list_software_OpenBabel_872` - :ref:`list_software_OpenBLAS_692` - :ref:`list_software_OpenCoarrays_1238` - :ref:`list_software_OpenColorIO_1065` - :ref:`list_software_OpenCV_555` - :ref:`list_software_opencv_contrib_1499` - :ref:`list_software_OpenEXR_641` - :ref:`list_software_OpenFOAM_693` - :ref:`list_software_OpenFOAM-Extend_1354` - :ref:`list_software_OpenImageIO_1037` - :ref:`list_software_OpenJPEG_696` - :ref:`list_software_OpenKIM-API_890` - :ref:`list_software_openkim-models_1444` - :ref:`list_software_OpenMM_556` - :ref:`list_software_OpenMolcas_1009` - :ref:`list_software_OpenMPI_632` - :ref:`list_software_OpenNLP_636` - :ref:`list_software_OpenPGM_630` - :ref:`list_software_openpyxl_895` - :ref:`list_software_OpenRefine_1003` - :ref:`list_software_OpenSlide_899` - :ref:`list_software_openslide-python_1682` - :ref:`list_software_OpenSSL_644` - :ref:`list_software_OPERA_375` - :ref:`list_software_OptiType_830` - :ref:`list_software_OptiX_500` - :ref:`list_software_OR-Tools_735` - :ref:`list_software_ORCA_293` - :ref:`list_software_OrfM_372` - :ref:`list_software_OrthoFinder_1124` - :ref:`list_software_OrthoMCL_744` - :ref:`list_software_OSU-Micro-Benchmarks_1865` - :ref:`list_software_OTF2_283` - :ref:`list_software_ownCloud_843` - :ref:`list_software_oxford_asl_1073` .. _list_software_Oases_507: *Oases* +++++++ Oases is a de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly. *homepage*: http://www.ebi.ac.uk/~zerbino/oases/ ========== ============= =============== version versionsuffix toolchain ========== ============= =============== ``0.2.08`` ``foss/2016b`` ``0.2.08`` ``-kmer_101`` ``intel/2017b`` ========== ============= =============== .. _list_software_OBITools_747: *OBITools* ++++++++++ The OBITools programs aims to help you to manipulate various data and sequence files in a convenient way using the Unix command line interface. They follow the standard Unix interface for command line program, allowing to chain a set of commands using the pipe mecanism. *homepage*: http://www.grenoble.prabi.fr/trac/OBITools ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.2.9`` ``-Python-2.7.11`` ``foss/2016a`` ========= ================== ============== .. _list_software_OCaml_460: *OCaml* +++++++ OCaml is a general purpose industrial-strength programming language with an emphasis on expressiveness and safety. Developed for more than 20 years at Inria it benefits from one of the most advanced type systems and supports functional, imperative and object-oriented styles of programming. *homepage*: http://ocaml.org/ ========== ============== version toolchain ========== ============== ``4.02.3`` ``foss/2016a`` ``4.07.1`` ``foss/2018b`` ========== ============== .. _list_software_Octave_610: *Octave* ++++++++ GNU Octave is a high-level interpreted language, primarily intended for numerical computations. *homepage*: http://www.gnu.org/software/octave/ ========= ============= ================================================ version versionsuffix toolchain ========= ============= ================================================ ``4.0.0`` ``foss/2016a`` ``4.0.3`` ``intel/2016b`` ``4.2.1`` ``foss/2018a``, ``intel/2016b``, ``intel/2017a`` ``4.2.1`` ``-mt`` ``intel/2017a`` ``4.2.2`` ``foss/2018a`` ``4.4.1`` ``foss/2018b`` ========= ============= ================================================ .. _list_software_OMA_221: *OMA* +++++ The OMA ('Orthologous MAtrix') project is a method and database for the inference of orthologs among complete genomes *homepage*: https://omabrowser.org/standalone/ ========= ========== version toolchain ========= ========== ``2.1.1`` ``system`` ========= ========== .. _list_software_OOMPA_380: *OOMPA* +++++++ OOMPA is a suite of R packages for the analysis of gene expression (RNA), proteomics profiling, and other high throughput molecular biology data. *homepage*: https://r-forge.r-project.org/projects/oompa ========= ============= =============== version versionsuffix toolchain ========= ============= =============== ``3.1.2`` ``-R-3.3.1`` ``intel/2016b`` ========= ============= =============== .. _list_software_OPARI2_429: *OPARI2* ++++++++ OPARI2, the successor of Forschungszentrum Juelich's OPARI, is a source-to-source instrumentation tool for OpenMP and hybrid codes. It surrounds OpenMP directives and runtime library calls with calls to the POMP2 measurement interface. *homepage*: https://www.score-p.org ========= ================= version toolchain ========= ================= ``2.0`` ``foss/2016a`` ``2.0.5`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_OpenBabel_872: *OpenBabel* +++++++++++ Open Babel is a chemical toolbox designed to speak the many languages of chemical data. It's an open, collaborative project allowing anyone to search, convert, analyze, or store data from molecular modeling, chemistry, solid-state materials, biochemistry, or related areas. *homepage*: http://openbabel.org ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``2.3.2`` ``-Python-2.7.11`` ``foss/2016a`` ``2.4.1`` ``-Python-2.7.14`` ``intel/2017b`` ``2.4.1`` ``-Python-2.7.15`` ``intel/2018b`` ``2.4.1`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================== =============== .. _list_software_OpenBLAS_692: *OpenBLAS* ++++++++++ OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version. *homepage*: http://xianyi.github.com/OpenBLAS/ ========== ================= ========================================================== version versionsuffix toolchain ========== ================= ========================================================== ``0.2.9`` ``-LAPACK-3.5.0`` ``GCC/4.8.3`` ``0.2.12`` ``-LAPACK-3.5.0`` ``GCC/4.9.2`` ``0.2.13`` ``-LAPACK-3.5.0`` ``GCC/4.8.4``, ``GCC/4.9.2`` ``0.2.14`` ``-LAPACK-3.5.0`` ``GNU/4.9.2-2.25``, ``GNU/4.9.3-2.25`` ``0.2.15`` ``-LAPACK-3.6.0`` ``GCC/4.9.3-2.25`` ``0.2.18`` ``-LAPACK-3.6.0`` ``GCC/4.9.4-2.25``, ``GCC/5.3.0-2.26``, ``GCC/5.4.0-2.26`` ``0.2.18`` ``-LAPACK-3.6.1`` ``GCC/5.4.0-2.26``, ``gompi/2016.07`` ``0.2.19`` ``-LAPACK-3.6.1`` ``gompi/2016.09`` ``0.2.19`` ``-LAPACK-3.7.0`` ``GCC/5.4.0-2.26``, ``GCC/6.3.0-2.27`` ``0.2.20`` ``GCC/5.4.0-2.26``, ``GCC/6.4.0-2.28``, ``GCC/7.2.0-2.29`` ``0.3.0`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30`` ``0.3.1`` ``GCC/7.3.0-2.30`` ``0.3.3`` ``GCC/8.2.0-2.31.1`` ``0.3.4`` ``GCC/8.2.0-2.31.1`` ``0.3.5`` ``GCC/8.2.0-2.31.1`` ``0.3.6`` ``GCC/8.3.0-2.32`` ``0.3.7`` ``GCC/8.3.0`` ========== ================= ========================================================== .. _list_software_OpenCoarrays_1238: *OpenCoarrays* ++++++++++++++ OpenCoarrays is an open-source software project that supports the coarray Fortran (CAF) parallel programming features of the Fortran 2008 standard and several features proposed for Fortran 2015 in the draft Technical Specification TS 18508 Additional Parallel Features in Fortran. *homepage*: https://github.com/sourceryinstitute/opencoarrays ========= =============== version toolchain ========= =============== ``1.9.0`` ``gompi/2017a`` ``2.2.0`` ``gompi/2018b`` ``2.8.0`` ``gompi/2019b`` ========= =============== .. _list_software_OpenColorIO_1065: *OpenColorIO* +++++++++++++ OpenColorIO (OCIO) is a complete color management solution geared towards motion picture production with an emphasis on visual effects and computer animation. *homepage*: http://opencolorio.org/ ========= ============== version toolchain ========= ============== ``1.1.0`` ``foss/2018b`` ========= ============== .. _list_software_OpenCV_555: *OpenCV* ++++++++ OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. *homepage*: http://opencv.org/ ========== ================== ================================================================ version versionsuffix toolchain ========== ================== ================================================================ ``2.4.12`` ``intel/2016a`` ``3.1.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``3.3.0`` ``-Python-2.7.13`` ``intel/2017a`` ``3.3.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``3.3.0`` ``-Python-3.6.1`` ``intel/2017a`` ``3.3.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``3.4.1`` ``-Python-2.7.14`` ``foss/2018a`` ``3.4.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``3.4.5`` ``-Python-2.7.15`` ``foss/2018b`` ``3.4.7`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a`` ``3.4.7`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``4.0.1`` ``-Python-2.7.15`` ``foss/2018b`` ``4.0.1`` ``-Python-3.6.6`` ``foss/2018b`` ========== ================== ================================================================ .. _list_software_opencv_contrib_1499: *opencv_contrib* ++++++++++++++++ OpenCV (Open Source Computer Vision Library) is an open source computer vision and machine learning software library. OpenCV was built to provide a common infrastructure for computer vision applications and to accelerate the use of machine perception in the commercial products. *homepage*: http://opencv.org/ ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``3.4.1`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================= ============== .. _list_software_OpenEXR_641: *OpenEXR* +++++++++ OpenEXR is a high dynamic-range (HDR) image file format developed by Industrial Light & Magic for use in computer imaging applications *homepage*: https://www.openexr.com/ ========= ================================ version toolchain ========= ================================ ``2.2.0`` ``intel/2016b``, ``intel/2017a`` ``2.3.0`` ``foss/2018b``, ``intel/2018b`` ``2.4.0`` ``GCCcore/8.3.0`` ========= ================================ .. _list_software_OpenFOAM_693: *OpenFOAM* ++++++++++ OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. *homepage*: https://www.openfoam.com/ ================ ================================================ version toolchain ================ ================================================ ``2.2.2`` ``intel/2016a``, ``intel/2017a`` ``2.2.x`` ``intel/2019a`` ``2.3.1`` ``intel/2017a`` ``2.4.0`` ``intel/2017a``, ``intel/2019a`` ``3.0.0`` ``foss/2016a`` ``3.0.1`` ``intel/2016b``, ``intel/2018a`` ``4.0`` ``foss/2016b``, ``intel/2016b`` ``4.1`` ``foss/2016b``, ``intel/2017a`` ``5.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``5.0-20180108`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``6`` ``foss/2018b``, ``foss/2019b``, ``intel/2018a`` ``7`` ``foss/2019b`` ``v1606+`` ``foss/2018b`` ``v1612+`` ``foss/2018b`` ``v1712`` ``foss/2017b``, ``intel/2017b`` ``v1806`` ``foss/2018b`` ``v1812`` ``foss/2018b`` ``v1906`` ``foss/2019b`` ``v1912`` ``foss/2019b`` ================ ================================================ .. _list_software_OpenFOAM-Extend_1354: *OpenFOAM-Extend* +++++++++++++++++ OpenFOAM is a free, open source CFD software package. OpenFOAM has an extensive range of features to solve anything from complex fluid flows involving chemical reactions, turbulence and heat transfer, to solid dynamics and electromagnetics. *homepage*: http://www.extend-project.de/ ======= ================== ================================= version versionsuffix toolchain ======= ================== ================================= ``3.1`` ``gimkl/2.11.5`` ``3.2`` ``gimkl/2.11.5``, ``intel/2016a`` ``4.0`` ``intel/2017a`` ``4.0`` ``-Python-2.7.16`` ``intel/2019b`` ======= ================== ================================= .. _list_software_OpenImageIO_1037: *OpenImageIO* +++++++++++++ OpenImageIO is a library for reading and writing images, and a bunch of related classes, utilities, and applications. *homepage*: https://openimageio.org/ ========== ================================ version toolchain ========== ================================ ``1.6.17`` ``intel/2016b`` ``1.7.17`` ``intel/2017a`` ``1.8.16`` ``foss/2018b``, ``intel/2018b`` ``2.0.12`` ``gompi/2019b``, ``iimpi/2019b`` ========== ================================ .. _list_software_OpenJPEG_696: *OpenJPEG* ++++++++++ OpenJPEG is an open-source JPEG 2000 codec written in C language. It has been developed in order to promote the use of JPEG 2000, a still-image compression standard from the Joint Photographic Experts Group (JPEG). Since may 2015, it is officially recognized by ISO/IEC and ITU-T as a JPEG 2000 Reference Software. *homepage*: http://www.openjpeg.org/ ========= ==================================== version toolchain ========= ==================================== ``2.1`` ``GCCcore/6.4.0`` ``2.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.3.1`` ``GCCcore/8.2.0`` ========= ==================================== .. _list_software_OpenKIM-API_890: *OpenKIM-API* +++++++++++++ Open Knowledgebase of Interatomic Models. OpenKIM is an API and a collection of interatomic models (potentials) for atomistic simulations. It is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild only installs the API, the models have to be installed by the user by running kim-api-collections-management install user MODELNAME or kim-api-collections-management install user OpenKIM to install them all. *homepage*: https://openkim.org/ ========= ================================================ version toolchain ========= ================================================ ``1.9.2`` ``foss/2016b``, ``foss/2017b`` ``1.9.7`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` ========= ================================================ .. _list_software_openkim-models_1444: *openkim-models* ++++++++++++++++ Open Knowledgebase of Interatomic Models. OpenKIM is an API and a collection of interatomic models (potentials) for atomistic simulations. It is a library that can be used by simulation programs to get access to the models in the OpenKIM database. This EasyBuild installs the models. The API itself is in the kim-api package. *homepage*: https://openkim.org/ ============ =============================== version toolchain ============ =============================== ``20190725`` ``foss/2019a``, ``intel/2019a`` ============ =============================== .. _list_software_OpenMM_556: *OpenMM* ++++++++ OpenMM is a toolkit for molecular simulation. *homepage*: http://openmm.org ========= ================= =============================== version versionsuffix toolchain ========= ================= =============================== ``7.1.1`` ``-Python-3.6.3`` ``intel/2017b`` ``7.4.1`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========= ================= =============================== .. _list_software_OpenMolcas_1009: *OpenMolcas* ++++++++++++ OpenMolcas is a quantum chemistry software package *homepage*: https://gitlab.com/Molcas/OpenMolcas ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``18.09`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================= =============== .. _list_software_OpenMPI_632: *OpenMPI* +++++++++ The Open MPI Project is an open source MPI implementation. *homepage*: http://www.open-mpi.org/ ========== ============= ==================================================================================================================== version versionsuffix toolchain ========== ============= ==================================================================================================================== ``1.6.5`` ``GCC/4.8.1``, ``GCC/4.8.2``, ``GCC/4.8.3`` ``1.6.5`` ``-no-OFED`` ``GCC/4.8.1``, ``GCC/4.8.2`` ``1.7.3`` ``GCC/4.8.2`` ``1.8.1`` ``GCC/4.8.3`` ``1.8.3`` ``GCC/4.9.2`` ``1.8.4`` ``GCC/4.8.4``, ``GCC/4.9.2`` ``1.8.5`` ``GNU/4.9.2-2.25`` ``1.8.6`` ``GNU/4.9.3-2.25`` ``1.8.8`` ``GNU/4.9.3-2.25`` ``1.10.1`` ``GCC/4.9.3-2.25`` ``1.10.2`` ``GCC/4.9.3-2.25``, ``GCC/5.3.0-2.26``, ``GCC/6.1.0-2.27``, ``PGI/16.3-GCC-4.9.3-2.25``, ``PGI/16.4-GCC-5.3.0-2.26`` ``1.10.3`` ``GCC/5.4.0-2.26``, ``GCC/6.1.0-2.27``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` ``1.10.4`` ``PGI/16.7-GCC-5.4.0-2.26``, ``iccifort/2016.3.210-GCC-4.9.3-2.25`` ``2.0.0`` ``GCC/5.2.0`` ``2.0.1`` ``GCC/6.2.0-2.27``, ``iccifort/2017.1.132-GCC-5.4.0-2.26`` ``2.0.2`` ``GCC/6.3.0-2.27``, ``iccifort/2017.1.132-GCC-6.3.0-2.27`` ``2.0.2`` ``-opa`` ``GCC/6.3.0-2.27`` ``2.1.0`` ``GCC/6.3.0-2.28`` ``2.1.1`` ``GCC/6.4.0-2.28``, ``gcccuda/2017b``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ``2.1.2`` ``GCC/6.4.0-2.28``, ``gcccuda/2018a``, ``iccifort/2018.1.163-GCC-6.4.0-2.28`` ``2.1.3`` ``iccifort/2018.2.199-GCC-6.4.0-2.28`` ``3.0.0`` ``GCC/7.2.0-2.29`` ``3.1.0`` ``GCC/7.3.0-2.30`` ``3.1.1`` ``GCC/7.3.0-2.30``, ``gcccuda/2018b``, ``iccifort/2018.3.222-GCC-7.3.0-2.30`` ``3.1.2`` ``GCC/8.2.0-2.31.1`` ``3.1.3`` ``GCC/8.2.0-2.31.1``, ``gcccuda/2019a``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``3.1.4`` ``GCC/8.3.0``, ``GCC/8.3.0-2.32``, ``gcccuda/2019b`` ``4.0.0`` ``GCC/8.2.0-2.31.1`` ``4.0.0`` ``-hpcx`` ``GCC/8.2.0-2.31.1`` ``4.0.1`` ``GCC/8.3.0-2.32`` ``4.0.2`` ``GCC/9.2.0-2.32`` ``system`` ``GCC/system-2.29`` ========== ============= ==================================================================================================================== .. _list_software_OpenNLP_636: *OpenNLP* +++++++++ The Apache OpenNLP library is a machine learning based toolkit for the processing of natural language text. *homepage*: https://opennlp.apache.org/ ========= ========== version toolchain ========= ========== ``1.8.1`` ``system`` ========= ========== .. _list_software_OpenPGM_630: *OpenPGM* +++++++++ OpenPGM is an open source implementation of the Pragmatic General Multicast (PGM) specification in RFC 3208 available at www.ietf.org. PGM is a reliable and scalable multicast protocol that enables receivers to detect loss, request retransmission of lost data, or notify an application of unrecoverable loss. PGM is a receiver-reliable protocol, which means the receiver is responsible for ensuring all data is received, absolving the sender of reception responsibility. *homepage*: http://code.google.com/p/openpgm/ =========== ============================================================================================================================================================================= version toolchain =========== ============================================================================================================================================================================= ``5.2.122`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` =========== ============================================================================================================================================================================= .. _list_software_openpyxl_895: *openpyxl* ++++++++++ A Python library to read/write Excel 2010 xlsx/xlsm files *homepage*: https://openpyxl.readthedocs.io ========= ================= version toolchain ========= ================= ``2.6.2`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_OpenRefine_1003: *OpenRefine* ++++++++++++ OpenRefine is a power tool that allows you to load data, understand it, clean it up, reconcile it, and augment it with data coming from the web. *homepage*: https://github.com/OpenRefine/OpenRefine ======= =================== ========== version versionsuffix toolchain ======= =================== ========== ``2.7`` ``-Java-1.8.0_144`` ``system`` ======= =================== ========== .. _list_software_OpenSlide_899: *OpenSlide* +++++++++++ OpenSlide is a C library that provides a simple interface to read whole-slide images (also known as virtual slides). *homepage*: https://openslide.org/ ========= ================= version toolchain ========= ================= ``3.4.1`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_openslide-python_1682: *openslide-python* ++++++++++++++++++ OpenSlide Python is a Python interface to the OpenSlide library. *homepage*: https://github.com/openslide/openslide-python ========= ================= version toolchain ========= ================= ``1.1.1`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_OpenSSL_644: *OpenSSL* +++++++++ The OpenSSL Project is a collaborative effort to develop a robust, commercial-grade, full-featured, and Open Source toolchain implementing the Secure Sockets Layer (SSL v2/v3) and Transport Layer Security (TLS v1) protocols as well as a full-strength general purpose cryptography library. *homepage*: http://www.openssl.org/ ========== ===================================================================== version toolchain ========== ===================================================================== ``1.0.1f`` ``GCC/4.8.2`` ``1.0.1k`` ``GCC/4.9.2`` ``1.0.1s`` ``foss/2016a``, ``intel/2016a`` ``1.0.2g`` ``GCCcore/4.9.3`` ``1.0.2h`` ``foss/2016.04``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``1.1.0c`` ``GCC/5.4.0-2.26`` ``1.1.0e`` ``intel/2016b`` ``1.1.0h`` ``GCCcore/7.3.0`` ``1.1.1b`` ``GCCcore/8.2.0`` ``1.1.1d`` ``GCCcore/8.3.0`` ========== ===================================================================== .. _list_software_OPERA_375: *OPERA* +++++++ An optimal genome scaffolding program *homepage*: https://sourceforge.net/projects/operasf ========= ================ =============================== version versionsuffix toolchain ========= ================ =============================== ``2.0.6`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` ========= ================ =============================== .. _list_software_OptiType_830: *OptiType* ++++++++++ OptiType is a novel HLA genotyping algorithm based on integer linear programming, capable of producing accurate 4-digit HLA genotyping predictions from NGS data by simultaneously selecting all major and minor HLA Class I alleles. *homepage*: https://github.com/FRED-2/OptiType ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.3.2`` ``-Python-2.7.15`` ``foss/2018b`` ``1.3.2`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================== ============== .. _list_software_OptiX_500: *OptiX* +++++++ OptiX is NVIDIA SDK for easy ray tracing performance. It provides a simple framework for accessing the GPU’s massive ray tracing power using state-of-the-art GPU algorithms. *homepage*: https://developer.nvidia.com/optix ========= ================== version toolchain ========= ================== ``3.8.0`` ``GNU/4.9.3-2.25`` ``3.9.0`` ``GNU/4.9.3-2.25`` ========= ================== .. _list_software_OR-Tools_735: *OR-Tools* ++++++++++ Google Optimization Tools (a.k.a., OR-Tools) is an open-source, fast and portable software suite for solving combinatorial optimization problems. *homepage*: https://developers.google.com/optimization/ ======= ================= ============== version versionsuffix toolchain ======= ================= ============== ``7.1`` ``-Python-3.7.2`` ``foss/2019a`` ======= ================= ============== .. _list_software_ORCA_293: *ORCA* ++++++ ORCA is a flexible, efficient and easy-to-use general purpose tool for quantum chemistry with specific emphasis on spectroscopic properties of open-shell molecules. It features a wide variety of standard quantum chemical methods ranging from semiempirical methods to DFT to single- and multireference correlated ab initio methods. It can also treat environmental and relativistic effects. *homepage*: https://orcaforum.kofo.mpg.de ====================== ================== =============== version versionsuffix toolchain ====================== ================== =============== ``3_0_2-linux_x86-64`` ``-OpenMPI-1.8.1`` ``system`` ``4.0.0.2`` ``-OpenMPI-2.0.2`` ``system`` ``4.0.1`` ``-OpenMPI-2.0.2`` ``system`` ``4.1.0`` ``-OpenMPI-3.1.3`` ``system`` ``4.2.0`` ``gompi/2019b`` ``4.2.1`` ``gompi/2019b`` ====================== ================== =============== .. _list_software_OrfM_372: *OrfM* ++++++ A simple and not slow open reading frame (ORF) caller. *homepage*: https://github.com/wwood/OrfM ========= ======================================== version toolchain ========= ======================================== ``0.6.1`` ``foss/2016b`` ``0.7.1`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ========= ======================================== .. _list_software_OrthoFinder_1124: *OrthoFinder* +++++++++++++ OrthoFinder is a fast, accurate and comprehensive platform for comparative genomics *homepage*: https://github.com/davidemms/OrthoFinder ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``2.2.7`` ``-Python-2.7.14`` ``intel/2018a`` ``2.3.3`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============== .. _list_software_OrthoMCL_744: *OrthoMCL* ++++++++++ OrthoMCL is a genome-scale algorithm for grouping orthologous protein sequences. *homepage*: http://orthomcl.org/ ========= ================ =============== version versionsuffix toolchain ========= ================ =============== ``1.4`` ``-Perl-5.24.0`` ``intel/2016b`` ``2.0.9`` ``-Perl-5.24.0`` ``intel/2016b`` ========= ================ =============== .. _list_software_OSU-Micro-Benchmarks_1865: *OSU-Micro-Benchmarks* ++++++++++++++++++++++ OSU Micro-Benchmarks *homepage*: http://mvapich.cse.ohio-state.edu/benchmarks/ ========= ============================== version toolchain ========= ============================== ``5.3.2`` ``foss/2016a``, ``foss/2017a`` ``5.6.2`` ``gompi/2019a`` ========= ============================== .. _list_software_OTF2_283: *OTF2* ++++++ The Open Trace Format 2 is a highly scalable, memory efficient event trace data format plus support library. It is the new standard trace format for Scalasca, Vampir, and TAU and is open for other tools. *homepage*: https://www.score-p.org ======= ============================== version toolchain ======= ============================== ``2.0`` ``foss/2016a``, ``foss/2017a`` ``2.2`` ``GCCcore/8.2.0`` ======= ============================== .. _list_software_ownCloud_843: *ownCloud* ++++++++++ The ownCloud Desktop Client is a tool to synchronize files from ownCloud Server with your computer. *homepage*: https://github.com/owncloud/client ========= ================= version toolchain ========= ================= ``2.4.3`` ``foss/2018b`` ``2.5.4`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_oxford_asl_1073: *oxford_asl* ++++++++++++ A command line tool for quantification of perfusion from ASL data *homepage*: https://github.com/ibme-qubic/oxford_asl ========= ========================== =============== version versionsuffix toolchain ========= ========================== =============== ``3.9.6`` ``-centos7-Python-2.7.13`` ``intel/2017a`` ========= ========================== =============== .. _list_software_letter_p: *P* --- :ref:`list_software_p11-kit_583` - :ref:`list_software_p4est_496` - :ref:`list_software_p4vasp_606` - :ref:`list_software_p7zip_506` - :ref:`list_software_packmol_743` - :ref:`list_software_PAML_298` - :ref:`list_software_pandas_631` - :ref:`list_software_pandas-datareader_1713` - :ref:`list_software_PANDAseq_685` - :ref:`list_software_Pandoc_597` - :ref:`list_software_Pango_501` - :ref:`list_software_PAPI_298` - :ref:`list_software_parallel_845` - :ref:`list_software_parallel-fastq-dump_1916` - :ref:`list_software_ParallelIO_965` - :ref:`list_software_parasail_845` - :ref:`list_software_Paraver_721` - :ref:`list_software_ParaView_799` - :ref:`list_software_PARI-GP_496` - :ref:`list_software_ParmEd_569` - :ref:`list_software_ParMETIS_677` - :ref:`list_software_ParMGridGen_1040` - :ref:`list_software_pasta_537` - :ref:`list_software_PaStiX_569` - :ref:`list_software_patchelf_839` - :ref:`list_software_path.py_708` - :ref:`list_software_pbbam_514` - :ref:`list_software_pbcopper_859` - :ref:`list_software_pbdagcon_830` - :ref:`list_software_pbmm2_478` - :ref:`list_software_pbs_python_1094` - :ref:`list_software_PBSuite_668` - :ref:`list_software_PCAngsd_640` - :ref:`list_software_PCC_214` - :ref:`list_software_PCL_223` - :ref:`list_software_PCMSolver_859` - :ref:`list_software_PCRaster_772` - :ref:`list_software_PCRE_298` - :ref:`list_software_PCRE2_348` - :ref:`list_software_PDT_232` - :ref:`list_software_PEAR_296` - :ref:`list_software_Perl_403` - :ref:`list_software_perl-app-cpanminus_1820` - :ref:`list_software_Perl4-CoreLibs_1287` - :ref:`list_software_PETSc_415` - :ref:`list_software_petsc4py_828` - :ref:`list_software_pftoolsV3_912` - :ref:`list_software_pFUnit_598` - :ref:`list_software_PGDSpider_834` - :ref:`list_software_PGI_224` - :ref:`list_software_PHASE_369` - :ref:`list_software_PHAST_384` - :ref:`list_software_PheWAS_520` - :ref:`list_software_PhiPack_672` - :ref:`list_software_PHLAT_377` - :ref:`list_software_phono3py_832` - :ref:`list_software_phonopy_781` - :ref:`list_software_PHYLIP_470` - :ref:`list_software_PhyloBayes-MPI_1299` - :ref:`list_software_phylokit_884` - :ref:`list_software_phylonaut_996` - :ref:`list_software_PhyML_458` - :ref:`list_software_phyx_457` - :ref:`list_software_picard_627` - :ref:`list_software_pigz_442` - :ref:`list_software_PIL_229` - :ref:`list_software_PileOMeth_871` - :ref:`list_software_Pillow_631` - :ref:`list_software_Pillow-SIMD_977` - :ref:`list_software_Pilon_514` - :ref:`list_software_PIMS_313` - :ref:`list_software_Pindel_604` - :ref:`list_software_pip_329` - :ref:`list_software_Pisces_615` - :ref:`list_software_piSvM_495` - :ref:`list_software_piSvM-JSC_764` - :ref:`list_software_pixman_653` - :ref:`list_software_pizzly_690` - :ref:`list_software_pkg-config_997` - :ref:`list_software_pkgconfig_952` - :ref:`list_software_PlaScope_791` - :ref:`list_software_PLAST_388` - :ref:`list_software_Platanus_840` - :ref:`list_software_Platypus_866` - :ref:`list_software_plc_319` - :ref:`list_software_PLINK_382` - :ref:`list_software_PLINKSEQ_615` - :ref:`list_software_Ploticus_851` - :ref:`list_software_plotly_676` - :ref:`list_software_plotly.py_955` - :ref:`list_software_PLplot_603` - :ref:`list_software_PLUMED_455` - :ref:`list_software_PLY_245` - :ref:`list_software_PMIx_350` - :ref:`list_software_PnetCDF_612` - :ref:`list_software_pocl_430` - :ref:`list_software_pomkl_547` - :ref:`list_software_pompi_549` - :ref:`list_software_poppler_770` - :ref:`list_software_popt_451` - :ref:`list_software_Porechop_832` - :ref:`list_software_poretools_999` - :ref:`list_software_Postgres-XL_1064` - :ref:`list_software_PostgreSQL_980` - :ref:`list_software_POT_243` - :ref:`list_software_POV-Ray_590` - :ref:`list_software_PPfold_581` - :ref:`list_software_ppl_332` - :ref:`list_software_pplacer_743` - :ref:`list_software_pplpy_565` - :ref:`list_software_PRANK_380` - :ref:`list_software_PRC_229` - :ref:`list_software_preseq_656` - :ref:`list_software_Primer3_674` - :ref:`list_software_PRINSEQ_546` - :ref:`list_software_printproto_1121` - :ref:`list_software_PRISMS-PF_673` - :ref:`list_software_ProbABEL_679` - :ref:`list_software_prodigal_850` - :ref:`list_software_PROJ_315` - :ref:`list_software_ProjectQ_808` - :ref:`list_software_prokka_648` - :ref:`list_software_prompt-toolkit_1493` - :ref:`list_software_proovread_978` - :ref:`list_software_propy_570` - :ref:`list_software_Proteinortho_1293` - :ref:`list_software_protobuf_881` - :ref:`list_software_protobuf-python_1600` - :ref:`list_software_pscom_546` - :ref:`list_software_PSI_236` - :ref:`list_software_PSI4_288` - :ref:`list_software_psmc_435` - :ref:`list_software_psmpi_553` - :ref:`list_software_psmpi2_603` - :ref:`list_software_PSolver_715` - :ref:`list_software_PSORTb_506` - :ref:`list_software_psrecord_866` - :ref:`list_software_pstoedit_876` - :ref:`list_software_psutil_673` - :ref:`list_software_psycopg2_823` - :ref:`list_software_ptemcee_739` - :ref:`list_software_PTESFinder_916` - :ref:`list_software_pubtcrs_771` - :ref:`list_software_pullseq_774` - :ref:`list_software_py_233` - :ref:`list_software_py-cpuinfo_1034` - :ref:`list_software_PyAMG_414` - :ref:`list_software_PyAPS3_480` - :ref:`list_software_pybedtools_1093` - :ref:`list_software_pyBigWig_802` - :ref:`list_software_pybind11_744` - :ref:`list_software_PyCairo_695` - :ref:`list_software_PyCharm_692` - :ref:`list_software_pycma_538` - :ref:`list_software_PyCogent_809` - :ref:`list_software_PyCUDA_486` - :ref:`list_software_PyDatastream_1231` - :ref:`list_software_pydicom_757` - :ref:`list_software_pydlpoly_893` - :ref:`list_software_pyEGA3_489` - :ref:`list_software_pyenchant_970` - :ref:`list_software_PyFFmpeg_766` - :ref:`list_software_pyFFTW_544` - :ref:`list_software_pyfits_671` - :ref:`list_software_PyFMI_421` - :ref:`list_software_PyFR_353` - :ref:`list_software_pygccxml_871` - :ref:`list_software_pyGIMLi_635` - :ref:`list_software_Pygments_855` - :ref:`list_software_PyGObject_871` - :ref:`list_software_pygrib_653` - :ref:`list_software_PyGTK_431` - :ref:`list_software_PyGTS_439` - :ref:`list_software_PyGWAS_507` - :ref:`list_software_pyhdf_539` - :ref:`list_software_pyiron_673` - :ref:`list_software_Pyke3_460` - :ref:`list_software_Pylint_640` - :ref:`list_software_pymatgen_869` - :ref:`list_software_pymatgen-db_1112` - :ref:`list_software_pymbar_651` - :ref:`list_software_pymemcache_1052` - :ref:`list_software_PyNAST_511` - :ref:`list_software_Pyomo_532` - :ref:`list_software_PyOpenGL_750` - :ref:`list_software_pyplusplus_1137` - :ref:`list_software_pyproj_676` - :ref:`list_software_pyqstem_787` - :ref:`list_software_PyQt_398` - :ref:`list_software_PyQt5_451` - :ref:`list_software_PyQtGraph_896` - :ref:`list_software_PyRETIS_592` - :ref:`list_software_pyringe_766` - :ref:`list_software_Pyro4_478` - :ref:`list_software_Pysam_522` - :ref:`list_software_pyScaf_614` - :ref:`list_software_PySCF_421` - :ref:`list_software_pyshp_564` - :ref:`list_software_Pysolar_746` - :ref:`list_software_pysqlite_891` - :ref:`list_software_PyStan_607` - :ref:`list_software_pystran_785` - :ref:`list_software_PyTables_804` - :ref:`list_software_pytest_681` - :ref:`list_software_PYTHIA_463` - :ref:`list_software_Python_642` - :ref:`list_software_python-igraph_1354` - :ref:`list_software_python-Levenshtein_1876` - :ref:`list_software_python-parasail_1564` - :ref:`list_software_pythran_774` - :ref:`list_software_PyTorch_713` - :ref:`list_software_PyYAML_508` - :ref:`list_software_PyZMQ_449` .. _list_software_p11-kit_583: *p11-kit* +++++++++ Provides a way to load and enumerate PKCS#11 modules. Provides a standard configuration setup for installing PKCS#11 modules in such a way that they're discoverable. Also solves problems with coordinating the use of PKCS#11 by different components or libraries living in the same process. *homepage*: http://p11-glue.freedesktop.org/p11-kit.html ========== ====================================================================== version toolchain ========== ====================================================================== ``0.23.2`` ``GCCcore/5.4.0``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``intel/2016a`` ========== ====================================================================== .. _list_software_p4est_496: *p4est* +++++++ p4est is a C library to manage a collection (a forest) of multiple connected adaptive quadtrees or octrees in parallel. *homepage*: http://www.p4est.org ======= =============== version toolchain ======= =============== ``2.2`` ``intel/2019a`` ======= =============== .. _list_software_p4vasp_606: *p4vasp* ++++++++ Visualization suite for VASP *homepage*: http://www.p4vasp.at/ ========== ================== ================================ version versionsuffix toolchain ========== ================== ================================ ``0.3.29`` ``-Python-2.7.11`` ``intel/2016a`` ``0.3.30`` ``-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` ``0.3.30`` ``-Python-2.7.15`` ``foss/2018b`` ========== ================== ================================ .. _list_software_p7zip_506: *p7zip* +++++++ p7zip is a quick port of 7z.exe and 7za.exe (command line version of 7zip) for Unix. 7-Zip is a file archiver with highest compression ratio. *homepage*: http://p7zip.sourceforge.net/ ========== =========================================================================== version toolchain ========== =========================================================================== ``9.38.1`` ``GCC/4.9.2``, ``system`` ``16.02`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2018a`` ========== =========================================================================== .. _list_software_packmol_743: *packmol* +++++++++ Packing Optimization for Molecular Dynamics Simulations *homepage*: http://m3g.iqm.unicamp.br/packmol ========== =============================== version toolchain ========== =============================== ``16.103`` ``intel/2016a`` ``18.013`` ``foss/2018a``, ``intel/2018a`` ========== =============================== .. _list_software_PAML_298: *PAML* ++++++ PAML is a package of programs for phylogenetic analyses of DNA or protein sequences using maximum likelihood. *homepage*: http://abacus.gene.ucl.ac.uk/software/paml.html ======== ========================================================== version toolchain ======== ========================================================== ``4.9i`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ======== ========================================================== .. _list_software_pandas_631: *pandas* ++++++++ pandas is an open source, BSD-licensed library providing high-performance, easy-to-use data structures and data analysis tools for the Python programming language. *homepage*: https://pypi.python.org/pypi/pandas/ ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``0.18.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``0.18.0`` ``-Python-3.5.1`` ``foss/2016a``, ``intel/2016a`` ``0.18.1`` ``-Python-2.7.12`` ``intel/2016b`` ``0.18.1`` ``-Python-3.5.2`` ``intel/2016b`` ``0.19.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``0.19.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` ``0.19.1`` ``-Python-2.7.12`` ``intel/2016b`` ``0.19.1`` ``-Python-3.5.2`` ``intel/2016b`` ``0.20.1`` ``-Python-3.6.1`` ``intel/2017a`` ``0.21.0`` ``-Python-2.7.13`` ``intel/2017a`` ``0.21.0`` ``-Python-3.6.3`` ``intel/2017b`` ========== ================== =============================== .. _list_software_pandas-datareader_1713: *pandas-datareader* +++++++++++++++++++ Up to date remote data access for pandas, works for multiple versions of pandas. *homepage*: https://pypi.org/project/pandas-datareader ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``0.7.0`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== .. _list_software_PANDAseq_685: *PANDAseq* ++++++++++ PANDASEQ is a program to align Illumina reads, optionally with PCR primers embedded in the sequence, and reconstruct an overlapping sequence. *homepage*: https://github.com/neufeld/pandaseq ======== ========================================================== version toolchain ======== ========================================================== ``2.10`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` ``2.11`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ======== ========================================================== .. _list_software_Pandoc_597: *Pandoc* ++++++++ If you need to convert files from one markup format into another, pandoc is your swiss-army knife *homepage*: http://pandoc.org ========= ========== version toolchain ========= ========== ``2.1.3`` ``system`` ``2.5`` ``system`` ========= ========== .. _list_software_Pango_501: *Pango* +++++++ Pango is a library for laying out and rendering of text, with an emphasis on internationalization. Pango can be used anywhere that text layout is needed, though most of the work on Pango so far has been done in the context of the GTK+ widget toolkit. Pango forms the core of text and font handling for GTK+-2.x. *homepage*: https://www.pango.org/ =========== ================================== version toolchain =========== ================================== ``1.39.0`` ``foss/2016a``, ``intel/2016a`` ``1.40.1`` ``foss/2016a``, ``intel/2016a`` ``1.40.3`` ``foss/2016b``, ``intel/2016b`` ``1.40.5`` ``intel/2017a`` ``1.40.12`` ``intel/2017a`` ``1.40.14`` ``foss/2017b``, ``intel/2017b`` ``1.41.0`` ``foss/2017b``, ``intel/2017b`` ``1.41.1`` ``foss/2018a``, ``intel/2018a`` ``1.42.4`` ``foss/2018b``, ``fosscuda/2018b`` ``1.43.0`` ``GCCcore/8.2.0`` =========== ================================== .. _list_software_PAPI_298: *PAPI* ++++++ PAPI provides the tool designer and application engineer with a consistent interface and methodology for use of the performance counter hardware found in most major microprocessors. PAPI enables software engineers to see, in near real time, the relation between software performance and processor events. In addition Component PAPI provides access to a collection of components that expose performance measurement opportunites across the hardware and software stack. *homepage*: http://icl.cs.utk.edu/projects/papi/ ========= ==================================== version toolchain ========= ==================================== ``5.4.3`` ``foss/2016a`` ``5.5.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``5.6.0`` ``GCCcore/6.4.0`` ``5.7.0`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ========= ==================================== .. _list_software_parallel_845: *parallel* ++++++++++ parallel: Build and execute shell commands in parallel *homepage*: https://savannah.gnu.org/projects/parallel/ ============ =============================== version toolchain ============ =============================== ``20141122`` ``GCC/4.9.2`` ``20150322`` ``GCC/4.9.2`` ``20150822`` ``GCC/4.9.2`` ``20160622`` ``foss/2016a`` ``20170822`` ``intel/2017a`` ``20171022`` ``intel/2017b`` ``20171122`` ``foss/2017b``, ``intel/2017b`` ``20180422`` ``intel/2018a`` ``20180822`` ``foss/2018b`` ``20181222`` ``intel/2018b`` ``20190222`` ``GCCcore/7.3.0`` ``20190622`` ``GCCcore/8.2.0`` ``20190922`` ``GCCcore/8.3.0`` ============ =============================== .. _list_software_parallel-fastq-dump_1916: *parallel-fastq-dump* +++++++++++++++++++++ parallel fastq-dump wrapper *homepage*: https://github.com/rvalieris/parallel-fastq-dump ========= ================= ================= version versionsuffix toolchain ========= ================= ================= ``0.6.5`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========= ================= ================= .. _list_software_ParallelIO_965: *ParallelIO* ++++++++++++ A high-level Parallel I/O Library for structured grid applications *homepage*: https://github.com/NCAR/ParallelIO ========== =============== version toolchain ========== =============== ``2.2.2a`` ``intel/2017a`` ========== =============== .. _list_software_parasail_845: *parasail* ++++++++++ parasail is a SIMD C (C99) library containing implementations of the Smith-Waterman (local), Needleman-Wunsch (global), and semi-global pairwise sequence alignment algorithms. *homepage*: https://github.com/jeffdaily/parasail ======= =============== version toolchain ======= =============== ``2.2`` ``intel/2018a`` ``2.4`` ``foss/2018b`` ======= =============== .. _list_software_Paraver_721: *Paraver* +++++++++ A very powerful performance visualization and analysis tool based on traces that can be used to analyse any information that is expressed on its input trace format. Traces for parallel MPI, OpenMP and other programs can be genereated with Extrae. *homepage*: https://tools.bsc.es/paraver ========= ============== version toolchain ========= ============== ``4.8.1`` ``foss/2019a`` ========= ============== .. _list_software_ParaView_799: *ParaView* ++++++++++ ParaView is a scientific parallel visualizer. *homepage*: https://www.paraview.org ========= ====================== ================================================================================================= version versionsuffix toolchain ========= ====================== ================================================================================================= ``4.4.0`` ``foss/2016a``, ``intel/2016a`` ``4.4.0`` ``-mpi`` ``gimkl/2.11.5`` ``5.1.2`` ``-mpi`` ``foss/2016b``, ``intel/2016b`` ``5.2.0`` ``-mpi`` ``foss/2016b``, ``intel/2017a`` ``5.3.0`` ``-mpi`` ``foss/2016b`` ``5.4.1`` ``-mpi`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``5.5.2`` ``-Python-2.7.15-mpi`` ``foss/2018b`` ``5.6.2`` ``-Python-3.7.4-mpi`` ``foss/2019b`` ========= ====================== ================================================================================================= .. _list_software_PARI-GP_496: *PARI-GP* +++++++++ PARI/GP is a widely used computer algebra system designed for fast computations in number theory (factorizations, algebraic number theory, elliptic curves...), but also contains a large number of other useful functions to compute with mathematical entities such as matrices, polynomials, power series, algebraic numbers etc., and a lot of transcendental functions. PARI is also available as a C library to allow for faster computations. *homepage*: http://pari.math.u-bordeaux.fr ========= ============== version toolchain ========= ============== ``2.7.6`` ``foss/2016a`` ========= ============== .. _list_software_ParmEd_569: *ParmEd* ++++++++ ParmEd is a general tool for aiding in investigations of biomolecular systems using popular molecular simulation packages, like Amber, CHARMM, and OpenMM written in Python. *homepage*: http://parmed.github.io/ParmEd/html/index.html ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``2.7.3`` ``-Python-3.6.3`` ``intel/2017b`` ========= ================= =============== .. _list_software_ParMETIS_677: *ParMETIS* ++++++++++ ParMETIS is an MPI-based parallel library that implements a variety of algorithms for partitioning unstructured graphs, meshes, and for computing fill-reducing orderings of sparse matrices. ParMETIS extends the functionality provided by METIS and includes routines that are especially suited for parallel AMR computations and large scale numerical simulations. The algorithms implemented in ParMETIS are based on the parallel multilevel k-way graph-partitioning, adaptive repartitioning, and parallel multi-constrained partitioning schemes. *homepage*: http://glaros.dtc.umn.edu/gkhome/metis/parmetis/overview ========= ========================================================================================================================================================================================================================================================================= version toolchain ========= ========================================================================================================================================================================================================================================================================= ``4.0.3`` ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``gimkl/2.11.5``, ``gompi/2019a``, ``iimpi/2019a``, ``iimpi/2019b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ========= ========================================================================================================================================================================================================================================================================= .. _list_software_ParMGridGen_1040: *ParMGridGen* +++++++++++++ ParMGridGen is an MPI-based parallel library that is based on the serial package MGridGen, that implements (serial) algorithms for obtaining a sequence of successive coarse grids that are well-suited for geometric multigrid methods. *homepage*: http://www-users.cs.umn.edu/~moulitsa/software.html ======= =================================================================== version toolchain ======= =================================================================== ``1.0`` ``gimkl/2.11.5``, ``iimpi/2019b``, ``intel/2016a``, ``intel/2017a`` ======= =================================================================== .. _list_software_pasta_537: *pasta* +++++++ PASTA (Practical Alignment using SATe and Transitivity) *homepage*: https://github.com/smirarab/pasta ========= ================= ==================== version versionsuffix toolchain ========= ================= ==================== ``1.8.5`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` ========= ================= ==================== .. _list_software_PaStiX_569: *PaStiX* ++++++++ PaStiX (Parallel Sparse matriX package) is a scientific library that provides a high performance parallel solver for very large sparse linear systems based on direct methods. *homepage*: http://pastix.gforge.inria.fr/ ========= ============== version toolchain ========= ============== ``5.2.3`` ``foss/2017b`` ========= ============== .. _list_software_patchelf_839: *patchelf* ++++++++++ PatchELF is a small utility to modify the dynamic linker and RPATH of ELF executables. *homepage*: http://nixos.org/patchelf.html ======== ================================= version toolchain ======== ================================= ``0.8`` ``GNU/4.9.3-2.25`` ``0.9`` ``GCCcore/6.4.0``, ``foss/2016a`` ``0.10`` ``GCCcore/7.2.0`` ======== ================================= .. _list_software_path.py_708: *path.py* +++++++++ path.py is a Python library implementing path objects as first-class entities, allowing common operations on files to be invoked on those path objects directly. *homepage*: https://github.com/jaraco/path.py ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``8.2.1`` ``-Python-2.7.11`` ``foss/2016a`` ``8.2.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``8.2.1`` ``-Python-3.5.1`` ``foss/2016a`` ``8.2.1`` ``-Python-3.5.2`` ``intel/2016b`` ``10.1`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============================== .. _list_software_pbbam_514: *pbbam* +++++++ The pbbam software package provides components to create, query, & edit PacBio BAM files and associated indices. *homepage*: http://pbbam.readthedocs.io/ ============ =============== version toolchain ============ =============== ``1.0.6`` ``gompi/2019a`` ``20170508`` ``intel/2017a`` ============ =============== .. _list_software_pbcopper_859: *pbcopper* ++++++++++ The pbcopper library provides a suite of data structures, algorithms, and utilities for C++ applications. *homepage*: https://github.com/PacificBiosciences/pbcopper ========= =============== version toolchain ========= =============== ``1.3.0`` ``gompi/2019a`` ========= =============== .. _list_software_pbdagcon_830: *pbdagcon* ++++++++++ pbdagcon is a tool that implements DAGCon (Directed Acyclic Graph Consensus) which is a sequence consensus algorithm based on using directed acyclic graphs to encode multiple sequence alignment. *homepage*: https://github.com/PacificBiosciences/pbdagcon ============ =============== version toolchain ============ =============== ``20170330`` ``intel/2017a`` ============ =============== .. _list_software_pbmm2_478: *pbmm2* +++++++ A minimap2 frontend for PacBio native data formats *homepage*: https://github.com/PacificBiosciences/pbmm2 ========= =============== version toolchain ========= =============== ``1.1.0`` ``gompi/2019a`` ========= =============== .. _list_software_pbs_python_1094: *pbs_python* ++++++++++++ The pbs_python package is a wrapper class for the Torque C library. With this package you now can write utilities/extensions in Python instead of C. We developed this package because we want to replace xpbsmon by an ascii version named pbsmon. PBSQuery is also included in this package. This is a python module build on top of the pbs python module to simplify querying the batch server, eg: how many jobs, how many nodes, ... *homepage*: https://oss.trac.surfsara.nl/pbs_python ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``4.6.0`` ``system`` ``4.6.0`` ``-Python-2.7.11`` ``intel/2016a`` ``4.6.0`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== .. _list_software_PBSuite_668: *PBSuite* +++++++++ PBJelly is a highly automated pipeline that aligns long sequencing reads (such as PacBio RS reads or long 454 reads in fasta format) to high-confidence draft assembles. *homepage*: https://sourceforge.net/p/pb-jelly/wiki/Home/ =========== ================== =============== version versionsuffix toolchain =========== ================== =============== ``15.8.24`` ``-Python-2.7.12`` ``intel/2016b`` =========== ================== =============== .. _list_software_PCAngsd_640: *PCAngsd* +++++++++ PCAngsd, which estimates the covariance matrix for low depth NGS data in an iterative procedure based on genotype likelihoods and is able to perform multiple population genetic analyses in heterogeneous populations. *homepage*: http://www.popgen.dk/software/index.php/PCAngsd ======== ================== ============== version versionsuffix toolchain ======== ================== ============== ``0.97`` ``-Python-2.7.14`` ``foss/2018a`` ======== ================== ============== .. _list_software_PCC_214: *PCC* +++++ The compiler is based on the original Portable C Compiler by S. C. Johnson, written in the late 70's. About 50% of the frontend code and 80% of the backend code has been modified. *homepage*: http://pcc.ludd.ltu.se/ ============ ========== version toolchain ============ ========== ``20131024`` ``system`` ============ ========== .. _list_software_PCL_223: *PCL* +++++ The Point Cloud Library (PCL) is a standalone, large scale, open project for 2D/3D image and point cloud processing. *homepage*: http://pointclouds.org/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.7.2`` ``-Python-2.7.11`` ``intel/2016a`` ``1.8.1`` ``-Python-2.7.14`` ``intel/2017b`` ========= ================== =============== .. _list_software_PCMSolver_859: *PCMSolver* +++++++++++ An API for the Polarizable Continuum Model. *homepage*: https://pcmsolver.readthedocs.org ============ ================== =============== version versionsuffix toolchain ============ ================== =============== ``1.1.4`` ``-Python-2.7.11`` ``intel/2016a`` ``1.2.3`` ``-Python-3.6.6`` ``foss/2018b`` ``1.2.3`` ``-Python-3.7.2`` ``gompi/2019a`` ``20160205`` ``-Python-2.7.11`` ``intel/2016a`` ============ ================== =============== .. _list_software_PCRaster_772: *PCRaster* ++++++++++ PCRaster Is a collection of software targeted at the development and deployment of spatio-temporal environmental models. *homepage*: http://pcraster.geo.uu.nl/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``4.1.0`` ``-Python-2.7.14`` ``intel/2017b`` ========= ================== =============== .. _list_software_PCRE_298: *PCRE* ++++++ The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. *homepage*: https://www.pcre.org/ ======== ================================================================================== version toolchain ======== ================================================================================== ``8.38`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``8.39`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` ``8.40`` ``GCCcore/6.3.0``, ``gimkl/2017a``, ``intel/2016b``, ``intel/2017a`` ``8.41`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``8.43`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ======== ================================================================================== .. _list_software_PCRE2_348: *PCRE2* +++++++ The PCRE library is a set of functions that implement regular expression pattern matching using the same syntax and semantics as Perl 5. *homepage*: https://www.pcre.org/ ========= ==================================== version toolchain ========= ==================================== ``10.21`` ``foss/2016a`` ``10.31`` ``foss/2018b`` ``10.33`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ==================================== .. _list_software_PDT_232: *PDT* +++++ Program Database Toolkit (PDT) is a framework for analyzing source code written in several programming languages and for making rich program knowledge accessible to developers of static and dynamic analysis tools. PDT implements a standard program representation, the program database (PDB), that can be accessed in a uniform way through a class library supporting common PDB operations. *homepage*: http://www.cs.uoregon.edu/research/pdt/ ======== ================= version toolchain ======== ================= ``3.22`` ``foss/2016a`` ``3.25`` ``GCCcore/8.2.0`` ======== ================= .. _list_software_PEAR_296: *PEAR* ++++++ PEAR is an ultrafast, memory-efficient and highly accurate pair-end read merger. It is fully parallelized and can run with as low as just a few kilobytes of memory. *homepage*: http://sco.h-its.org/exelixis/web/software/pear/ ========== ========================================================== version toolchain ========== ========================================================== ``0.9.8`` ``foss/2016b``, ``intel/2016b`` ``0.9.10`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ``0.9.11`` ``GCCcore/7.3.0``, ``foss/2018a`` ========== ========================================================== .. _list_software_Perl_403: *Perl* ++++++ Larry Wall's Practical Extraction and Report Language *homepage*: https://www.perl.org/ ========== ============= ========================================================================================= version versionsuffix toolchain ========== ============= ========================================================================================= ``5.20.1`` ``-bare`` ``GCC/4.8.2``, ``GCC/4.9.2`` ``5.20.2`` ``-bare`` ``GCC/4.9.2`` ``5.20.3`` ``foss/2016a``, ``intel/2016a`` ``5.22.0`` ``-bare`` ``GCC/4.9.2`` ``5.22.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` ``5.22.1`` ``-bare`` ``foss/2016a``, ``intel/2016a`` ``5.22.2`` ``intel/2016a`` ``5.24.0`` ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` ``5.24.0`` ``-bare`` ``foss/2016b`` ``5.24.1`` ``GCCcore/6.3.0``, ``foss/2017a``, ``intel/2017a`` ``5.26.0`` ``GCCcore/6.4.0``, ``foss/2017b``, ``intel/2017b``, ``intel/2018.00``, ``intel/2018.01`` ``5.26.1`` ``GCCcore/6.4.0``, ``foss/2018a`` ``5.26.1`` ``-bare`` ``foss/2018a`` ``5.28.0`` ``GCCcore/7.3.0`` ``5.28.1`` ``GCCcore/8.2.0`` ``5.30.0`` ``GCCcore/8.3.0`` ========== ============= ========================================================================================= .. _list_software_perl-app-cpanminus_1820: *perl-app-cpanminus* ++++++++++++++++++++ cpanm - get, unpack build and install modules from CPAN *homepage*: https://github.com/miyagawa/cpanminus ========== ========== version toolchain ========== ========== ``1.7039`` ``system`` ========== ========== .. _list_software_Perl4-CoreLibs_1287: *Perl4-CoreLibs* ++++++++++++++++ Libraries historically supplied with Perl 4 *homepage*: https://metacpan.org/pod/Perl4::CoreLibs ========= ================ =============== version versionsuffix toolchain ========= ================ =============== ``0.003`` ``-Perl-5.24.1`` ``intel/2017a`` ========= ================ =============== .. _list_software_PETSc_415: *PETSc* +++++++ PETSc, pronounced PET-see (the S is silent), is a suite of data structures and routines for the scalable (parallel) solution of scientific applications modeled by partial differential equations. *homepage*: http://www.mcs.anl.gov/petsc ========== ==================== =============================== version versionsuffix toolchain ========== ==================== =============================== ``3.7.2`` ``-Python-2.7.11`` ``intel/2016a`` ``3.7.3`` ``-Python-2.7.11`` ``foss/2016a`` ``3.7.5`` ``-downloaded-deps`` ``intel/2016b`` ``3.8.3`` ``-downloaded-deps`` ``foss/2017b`` ``3.9.1`` ``-downloaded-deps`` ``foss/2018a`` ``3.9.3`` ``foss/2018a``, ``intel/2018a`` ``3.11.0`` ``-downloaded-deps`` ``foss/2018b`` ``3.11.1`` ``foss/2019a``, ``intel/2019a`` ========== ==================== =============================== .. _list_software_petsc4py_828: *petsc4py* ++++++++++ petsc4py are Python bindings for PETSc, the Portable, Extensible Toolchain for Scientific Computation. *homepage*: https://bitbucket.org/petsc/petsc4py ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``3.9.1`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================= ============== .. _list_software_pftoolsV3_912: *pftoolsV3* +++++++++++ The pftools package contains all the software necessary to build protein and DNA generalized profiles and use them to scan and align sequences, and search databases. *homepage*: http://web.expasy.org/pftools/ ============ ============== version toolchain ============ ============== ``20160324`` ``foss/2016a`` ============ ============== .. _list_software_pFUnit_598: *pFUnit* ++++++++ pFUnit is a unit testing framework enabling JUnit-like testing of serial and MPI-parallel software written in Fortran. *homepage*: http://pfunit.sourceforge.net ========= =============== version toolchain ========= =============== ``3.2.9`` ``gompi/2018b`` ========= =============== .. _list_software_PGDSpider_834: *PGDSpider* +++++++++++ An automated data conversion tool for connecting population genetics and genomics programs *homepage*: http://cmpg.unibe.ch/software/PGDSpider/ =========== ================== ========== version versionsuffix toolchain =========== ================== ========== ``2.1.0.3`` ``-Java-1.7.0_80`` ``system`` =========== ================== ========== .. _list_software_PGI_224: *PGI* +++++ C, C++ and Fortran compilers from The Portland Group - PGI *homepage*: https://www.pgroup.com/ ========= ======================= ========== version versionsuffix toolchain ========= ======================= ========== ``15.7`` ``-GNU-4.9.2-2.25`` ``system`` ``15.7`` ``-GNU-4.9.3-2.25`` ``system`` ``15.10`` ``-GCC-4.9.3-2.25`` ``system`` ``16.1`` ``-CDK-GCC-4.9.2-2.25`` ``system`` ``16.3`` ``-GCC-4.9.3-2.25`` ``system`` ``16.4`` ``-GCC-5.3.0-2.26`` ``system`` ``16.7`` ``-GCC-5.4.0-2.26`` ``system`` ``16.10`` ``-GCC-5.4.0-2.26`` ``system`` ``17.1`` ``-GCC-6.3.0-2.27`` ``system`` ``17.3`` ``-GCC-6.3.0-2.28`` ``system`` ``17.4`` ``-GCC-6.4.0-2.28`` ``system`` ``17.10`` ``-GCC-6.4.0-2.28`` ``system`` ``18.1`` ``-GCC-7.2.0-2.29`` ``system`` ``18.4`` ``-GCC-6.4.0-2.28`` ``system`` ``18.7`` ``-GCC-7.3.0-2.30`` ``system`` ``18.10`` ``-GCC-6.4.0-2.28`` ``system`` ``19.1`` ``-GCC-8.2.0-2.31.1`` ``system`` ``19.4`` ``-GCC-8.2.0-2.31.1`` ``system`` ``19.7`` ``-GCC-8.3.0-2.32`` ``system`` ========= ======================= ========== .. _list_software_PHASE_369: *PHASE* +++++++ The program PHASE implements a Bayesian statistical method for reconstructing haplotypes from population genotype data. Documentation: http://stephenslab.uchicago.edu/assets/software/phase/instruct2.1.pdf *homepage*: http://stephenslab.uchicago.edu/phase/download.html ========= ========== version toolchain ========= ========== ``2.1.1`` ``system`` ========= ========== .. _list_software_PHAST_384: *PHAST* +++++++ PHAST is a freely available software package for comparative and evolutionary genomics. *homepage*: http://compgen.cshl.edu/phast/ ======= ========================================================== version toolchain ======= ========================================================== ``1.4`` ``intel/2017a`` ``1.5`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ======= ========================================================== .. _list_software_PheWAS_520: *PheWAS* ++++++++ Provides an accessible R interface to the phenome wide association study. *homepage*: https://www.vumc.org/cpm/center-precision-medicine-blog/phewas-r-package ============ ============= =============================== version versionsuffix toolchain ============ ============= =============================== ``0.12`` ``-R-3.3.3`` ``foss/2016b``, ``intel/2016b`` ``0.99.5-2`` ``-R-3.6.0`` ``foss/2019a``, ``intel/2019a`` ============ ============= =============================== .. _list_software_PhiPack_672: *PhiPack* +++++++++ The PhiPack software package implements (in C) a few tests for recombination and can produce refined incompatibility matrices as well. *homepage*: http://www.maths.otago.ac.nz/~dbryant/software.html ============== ======================================== version toolchain ============== ======================================== ``2016.06.14`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ============== ======================================== .. _list_software_PHLAT_377: *PHLAT* +++++++ PHLAT is a bioinformatics algorithm that offers HLA typing at four-digit resolution (or higher) using genome-wide transcriptome and exome sequencing data over a wide range of read lengths and sequencing depths. *homepage*: https://sites.google.com/site/phlatfortype/ ======= ================== ============== version versionsuffix toolchain ======= ================== ============== ``1.1`` ``-Python-2.7.15`` ``foss/2018b`` ======= ================== ============== .. _list_software_phono3py_832: *phono3py* ++++++++++ phono3py calculates phonon-phonon interaction and related properties using the supercell approach. *homepage*: http://atztogo.github.io/phono3py/ ============= ================== =============================== version versionsuffix toolchain ============= ================== =============================== ``1.12.5.35`` ``-Python-2.7.14`` ``intel/2017b`` ``1.12.7.55`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ============= ================== =============================== .. _list_software_phonopy_781: *phonopy* +++++++++ Phonopy is an open source package of phonon calculations based on the supercell approach. *homepage*: http://atztogo.github.io/phonopy/ ============= ================== =============================== version versionsuffix toolchain ============= ================== =============================== ``1.10.1`` ``-Python-2.7.11`` ``intel/2016a`` ``1.12.2.20`` ``-Python-2.7.14`` ``intel/2017b`` ``1.12.6.66`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``1.13.0.64`` ``-Python-2.7.14`` ``intel/2018a`` ``1.14.2`` ``-Python-2.7.15`` ``intel/2018b`` ``2.0.0`` ``-Python-2.7.14`` ``intel/2018a`` ``2.2.0`` ``-Python-3.7.2`` ``intel/2019a`` ============= ================== =============================== .. _list_software_PHYLIP_470: *PHYLIP* ++++++++ PHYLIP is a free package of programs for inferring phylogenies. *homepage*: http://evolution.genetics.washington.edu/phylip ========= ========================================================== version toolchain ========= ========================================================== ``3.696`` ``foss/2016a``, ``intel/2016a`` ``3.697`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ========= ========================================================== .. _list_software_PhyloBayes-MPI_1299: *PhyloBayes-MPI* ++++++++++++++++ A Bayesian software for phylogenetic reconstruction using mixture models *homepage*: https://github.com/bayesiancook/pbmpi ============ =============== version toolchain ============ =============== ``20161021`` ``intel/2016b`` ============ =============== .. _list_software_phylokit_884: *phylokit* ++++++++++ C++ library for high performance phylogenetics *homepage*: https://github.com/pranjalv123/phylokit ======= ==================== version toolchain ======= ==================== ``1.0`` ``GCC/8.2.0-2.31.1`` ======= ==================== .. _list_software_phylonaut_996: *phylonaut* +++++++++++ Dynamic programming for phylogenetics applications *homepage*: https://github.com/pranjalv123/phylonaut ============ =============== version toolchain ============ =============== ``20190626`` ``gompi/2019a`` ============ =============== .. _list_software_PhyML_458: *PhyML* +++++++ Phylogenetic estimation using (Maximum) Likelihood *homepage*: https://github.com/stephaneguindon/phyml ================ ============== version toolchain ================ ============== ``3.3.20190321`` ``foss/2018b`` ================ ============== .. _list_software_phyx_457: *phyx* ++++++ phyx performs phylogenetics analyses on trees and sequences. *homepage*: https://github.com/FePhyFoFum/phyx ======== ============== version toolchain ======== ============== ``1.01`` ``foss/2019a`` ======== ============== .. _list_software_picard_627: *picard* ++++++++ A set of tools (in Java) for working with next generation sequencing data in the BAM format. *homepage*: http://sourceforge.net/projects/picard =========== =================== ========== version versionsuffix toolchain =========== =================== ========== ``1.39`` ``system`` ``1.100`` ``system`` ``1.109`` ``system`` ``1.119`` ``system`` ``1.119`` ``-Java-1.7.0_80`` ``system`` ``1.120`` ``-Java-1.8.0_66`` ``system`` ``1.141`` ``-Java-1.8.0_74`` ``system`` ``2.0.1`` ``-Java-1.8.0_66`` ``system`` ``2.1.0`` ``system`` ``2.1.0`` ``-Java-1.8.0_74`` ``system`` ``2.1.1`` ``-Java-1.8.0_112`` ``system`` ``2.1.1`` ``-Java-1.8.0_74`` ``system`` ``2.2.4`` ``-Java-1.8.0_92`` ``system`` ``2.6.0`` ``-Java-1.8.0_131`` ``system`` ``2.10.1`` ``-Java-1.8.0_131`` ``system`` ``2.18.5`` ``-Java-1.8.0_162`` ``system`` ``2.18.11`` ``-Java-1.8.0_162`` ``system`` ``2.18.14`` ``-Java-1.8`` ``system`` ``2.18.17`` ``-Java-1.8`` ``system`` ``2.18.27`` ``-Java-1.8`` ``system`` ``2.21.1`` ``-Java-11`` ``system`` =========== =================== ========== .. _list_software_pigz_442: *pigz* ++++++ pigz, which stands for parallel implementation of gzip, is a fully functional replacement for gzip that exploits multiple processors and multiple cores to the hilt when compressing data. pigz was written by Mark Adler, and uses the zlib and pthread libraries. *homepage*: https://zlib.net/pigz/ ========= ======================================================================= version toolchain ========= ======================================================================= ``2.3.3`` ``foss/2016b`` ``2.3.4`` ``GCCcore/6.4.0`` ``2.4`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2018a`` ========= ======================================================================= .. _list_software_PIL_229: *PIL* +++++ The Python Imaging Library (PIL) adds image processing capabilities to your Python interpreter. This library supports many file formats, and provides powerful image processing and graphics capabilities. *homepage*: http://www.pythonware.com/products/pil ========= ================================= =============================== version versionsuffix toolchain ========= ================================= =============================== ``1.1.7`` ``-Python-2.7.11`` ``intel/2016a`` ``1.1.7`` ``-Python-2.7.11-freetype-2.6.3`` ``intel/2016a`` ``1.1.7`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``1.1.7`` ``-Python-2.7.13`` ``intel/2017a`` ``1.1.7`` ``-Python-2.7.15`` ``foss/2019a`` ========= ================================= =============================== .. _list_software_PileOMeth_871: *PileOMeth* +++++++++++ PileOMeth processes a coordinate-sorted and indexed BAM or CRAM file containing some form of BS-seq alignments. PileOMeth extracts per-base methylation metrics from them. PileOMeth requires an indexed fasta file containing the reference genome as well. *homepage*: https://github.com/dpryan79/PileOMeth ========== ============== version toolchain ========== ============== ``0.1.11`` ``foss/2016b`` ========== ============== .. _list_software_Pillow_631: *Pillow* ++++++++ Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. *homepage*: https://pillow.readthedocs.org/ ========= ================================= =================================================== version versionsuffix toolchain ========= ================================= =================================================== ``3.2.0`` ``-Python-2.7.11`` ``intel/2016a`` ``3.2.0`` ``-Python-2.7.11-freetype-2.6.3`` ``foss/2016a``, ``intel/2016a`` ``3.4.2`` ``-Python-2.7.12`` ``intel/2016b`` ``3.4.2`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` ``3.4.2`` ``-Python-3.5.2-freetype-2.6.5`` ``intel/2016b`` ``4.1.0`` ``-Python-2.7.13`` ``intel/2017a`` ``4.1.1`` ``-Python-3.6.1`` ``intel/2017a`` ``4.2.1`` ``-Python-3.6.1`` ``intel/2017a`` ``4.3.0`` ``-Python-2.7.13`` ``intel/2017a`` ``4.3.0`` ``-Python-2.7.14`` ``intel/2017b`` ``4.3.0`` ``-Python-3.6.3`` ``foss/2017b`` ``5.0.0`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``5.0.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``5.0.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``5.3.0`` ``-Python-2.7.15`` ``foss/2018b`` ``5.3.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``6.0.0`` ``GCCcore/8.2.0`` ``6.2.1`` ``GCCcore/8.3.0`` ========= ================================= =================================================== .. _list_software_Pillow-SIMD_977: *Pillow-SIMD* +++++++++++++ Pillow is the 'friendly PIL fork' by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lundh and Contributors. *homepage*: https://github.com/uploadcare/pillow-simd =============== ================= =================================================== version versionsuffix toolchain =============== ================= =================================================== ``5.0.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``5.3.0.post0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``6.0.x.post0`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` =============== ================= =================================================== .. _list_software_Pilon_514: *Pilon* +++++++ Pilon is an automated genome assembly improvement and variant detection tool *homepage*: https://github.com/broadinstitute/pilon ======== =================== ========== version versionsuffix toolchain ======== =================== ========== ``1.22`` ``-Java-1.8`` ``system`` ``1.22`` ``-Java-1.8.0_162`` ``system`` ``1.23`` ``-Java-1.8`` ``system`` ``1.23`` ``-Java-11`` ``system`` ======== =================== ========== .. _list_software_PIMS_313: *PIMS* ++++++ PIMS is a lazy-loading interface to sequential data with numpy-like slicing. *homepage*: http://soft-matter.github.io/pims ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.4.1`` ``-Python-2.7.14`` ``intel/2017b`` ========= ================== =============== .. _list_software_Pindel_604: *Pindel* ++++++++ Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads. *homepage*: http://gmt.genome.wustl.edu/packages/pindel/ ==================== ================== version toolchain ==================== ================== ``0.2.5b8`` ``foss/2016b`` ``0.2.5b9-20170508`` ``GCC/6.4.0-2.28`` ==================== ================== .. _list_software_pip_329: *pip* +++++ The PyPA recommended tool for installing Python packages. *homepage*: https://pip.pypa.io ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``8.0.2`` ``-Python-2.7.11`` ``intel/2016a`` ``8.1.2`` ``-Python-2.7.11`` ``foss/2016a`` ``8.1.2`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ========= ================== =============================== .. _list_software_Pisces_615: *Pisces* ++++++++ Somatic and germline variant caller for amplicon data. Recommended caller for tumor-only workflows. *homepage*: https://github.com/Illumina/Pisces ============ ================= version toolchain ============ ================= ``5.2.7.47`` ``GCCcore/6.4.0`` ============ ================= .. _list_software_piSvM_495: *piSvM* +++++++ piSvM is a parallel implementation of the Support Vector Machine (SVM) algorithm that allows efficient training and testing on a multiprocessor system. *homepage*: http://pisvm.sourceforge.net/ ======= =============== version toolchain ======= =============== ``1.3`` ``intel/2017b`` ======= =============== .. _list_software_piSvM-JSC_764: *piSvM-JSC* +++++++++++ piSvM is a parallel implementation of the Support Vector Machine (SVM) algorithm that allows efficient training and testing on a multiprocessor system. This version is a fork of the original PiSvM to increase scalability. *homepage*: https://github.com/mricherzhagen/pisvm ================ =============== version toolchain ================ =============== ``1.2-20150622`` ``intel/2017b`` ================ =============== .. _list_software_pixman_653: *pixman* ++++++++ Pixman is a low-level software library for pixel manipulation, providing features such as image compositing and trapezoid rasterization. Important users of pixman are the cairo graphics library and the X server. *homepage*: http://www.pixman.org/ ========== ============================================================================================================================================ version toolchain ========== ============================================================================================================================================ ``0.34.0`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``0.38.0`` ``GCCcore/8.2.0`` ``0.38.4`` ``GCCcore/8.3.0`` ========== ============================================================================================================================================ .. _list_software_pizzly_690: *pizzly* ++++++++ Pizzly is a program for detecting gene fusions from RNA-Seq data of cancer samples. *homepage*: https://github.com/pmelsted/pizzly ========== ============== version toolchain ========== ============== ``0.37.3`` ``foss/2018b`` ========== ============== .. _list_software_pkg-config_997: *pkg-config* ++++++++++++ pkg-config is a helper tool used when compiling applications and libraries. It helps you insert the correct compiler options on the command line so an application can use gcc -o test test.c `pkg-config --libs --cflags glib-2.0` for instance, rather than hard-coding values on where to find glib (or other libraries). *homepage*: http://www.freedesktop.org/wiki/Software/pkg-config/ ========== =========================================================================================================================================================================== version toolchain ========== =========================================================================================================================================================================== ``0.28`` ``GCC/4.8.2``, ``GCC/4.9.2``, ``GNU/4.9.3-2.25`` ``0.29`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``0.29.1`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``0.29.2`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a``, ``system`` ========== =========================================================================================================================================================================== .. _list_software_pkgconfig_952: *pkgconfig* +++++++++++ pkgconfig is a Python module to interface with the pkg-config command line tool *homepage*: https://github.com/matze/pkgconfig ========= ================== =================================================== version versionsuffix toolchain ========= ================== =================================================== ``1.1.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``1.1.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``1.1.0`` ``-Python-3.5.1`` ``foss/2016a`` ``1.1.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` ``1.2.2`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` ``1.2.2`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b`` ``1.2.2`` ``-Python-3.6.1`` ``foss/2017a``, ``intel/2017a`` ``1.2.2`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b`` ``1.3.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``1.3.1`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``1.3.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.3.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``1.5.1`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ``1.5.1`` ``-python`` ``GCCcore/8.2.0`` ========= ================== =================================================== .. _list_software_PlaScope_791: *PlaScope* ++++++++++ Plasmid exploration of bacterial genomes *homepage*: https://github.com/GuilhemRoyer/PlaScope ========= ============== version toolchain ========= ============== ``1.3.1`` ``foss/2018b`` ========= ============== .. _list_software_PLAST_388: *PLAST* +++++++ PLAST is a parallel alignment search tool for comparing large protein banks *homepage*: http://www.irisa.fr/symbiose/projects/plast/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.3.1`` ``-Java-1.8.0_92`` ``foss/2016a`` ========= ================== ============== .. _list_software_Platanus_840: *Platanus* ++++++++++ PLATform for Assembling NUcleotide Sequences *homepage*: http://platanus.bio.titech.ac.jp/ ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``1.2.1`` ``-linux-x86_64`` ``system`` ``1.2.4`` ``foss/2017a`` ========= ================= ============== .. _list_software_Platypus_866: *Platypus* ++++++++++ Platypus is a tool designed for efficient and accurate variant-detection in high-throughput sequencing data. *homepage*: http://www.well.ox.ac.uk/platypus ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.8.1`` ``-Python-2.7.11`` ``intel/2016a`` ========= ================== =============== .. _list_software_plc_319: *plc* +++++ plc is the public Planck Likelihood Code. It provides C and Fortran libraries that allow users to compute the log likelihoods of the temperature, polarization, and lensing maps. Optionally, it also provides a python version of this library, as well as tools to modify the predetermined options for some likelihoods (e.g. changing the high-ell and low-ell lmin and lmax values of the temperature). *homepage*: http://pla.esac.esa.int/pla/#home ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``3.0.1`` ``-Python-2.7.15`` ``foss/2019a``, ``intel/2018b`` ========= ================== =============================== .. _list_software_PLINK_382: *PLINK* +++++++ Whole-genome association analysis toolset *homepage*: https://www.cog-genomics.org/plink/2.0/ =========================== ============================== version toolchain =========================== ============================== ``1.07`` ``foss/2016a``, ``foss/2016b`` ``1.07-x86_64`` ``system`` ``1.9b_4.1-x86_64`` ``system`` ``2.00-alpha1-x86_64`` ``system`` ``2.00-alpha2-x86_64`` ``system`` ``2.00-alpha2-x86_64_avx2`` ``system`` =========================== ============================== .. _list_software_PLINKSEQ_615: *PLINKSEQ* ++++++++++ PLINK/SEQ is an open-source C/C++ library for working with human genetic variation data. The specific focus is to provide a platform for analytic tool development for variation data from large-scale resequencing and genotyping projects, particularly whole-exome and whole-genome studies. It is independent of (but designed to be complementary to) the existing PLINK package. *homepage*: https://atgu.mgh.harvard.edu/plinkseq/ ======== ========================================================== version toolchain ======== ========================================================== ``0.10`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ======== ========================================================== .. _list_software_Ploticus_851: *Ploticus* ++++++++++ Ploticus is a free GPL software utility that can produce various types of plots and graphs *homepage*: http://ploticus.sourceforge.net/doc/welcome.html ======== ================= version toolchain ======== ================= ``2.42`` ``GCCcore/7.3.0`` ======== ================= .. _list_software_plotly_676: *plotly* ++++++++ Easily translate 'ggplot2' graphs to an interactive web-based version and/or create custom web-based visualizations directly from R. *homepage*: https://cran.r-project.org/web/packages/plotly ========= ============= =============== version versionsuffix toolchain ========= ============= =============== ``4.7.1`` ``-R-3.4.0`` ``intel/2017a`` ``4.8.0`` ``-R-3.4.4`` ``intel/2018a`` ========= ============= =============== .. _list_software_plotly.py_955: *plotly.py* +++++++++++ An open-source, interactive graphing library for Python *homepage*: https://plot.ly/python ========= =============== version toolchain ========= =============== ``4.1.0`` ``intel/2019a`` ``4.4.1`` ``intel/2019b`` ========= =============== .. _list_software_PLplot_603: *PLplot* ++++++++ PLplot is a cross-platform software package for creating scientific plots whose (UTF-8) plot symbols and text are limited in practice only by what Unicode-aware system fonts are installed on a user's computer. *homepage*: http://plplot.sourceforge.net ========== ================================ =============== version versionsuffix toolchain ========== ================================ =============== ``5.11.1`` ``-Java-1.7.0_80-Python-2.7.11`` ``foss/2016a`` ``5.11.1`` ``-Java-1.7.0_80-Python-2.7.12`` ``intel/2016b`` ========== ================================ =============== .. _list_software_PLUMED_455: *PLUMED* ++++++++ PLUMED is an open source library for free energy calculations in molecular systems which works together with some of the most popular molecular dynamics engines. Free energy calculations can be performed as a function of many order parameters with a particular focus on biological problems, using state of the art methods such as metadynamics, umbrella sampling and Jarzynski-equation based steered MD. The software, written in C++, can be easily interfaced with both fortran and C/C++ codes. *homepage*: http://www.plumed-code.org ========= ================== ================================================ version versionsuffix toolchain ========= ================== ================================================ ``2.2.2`` ``intel/2016a`` ``2.2.3`` ``foss/2016b``, ``intel/2016b`` ``2.3.0`` ``foss/2016b``, ``foss/2017a``, ``intel/2016b`` ``2.3.4`` ``intel/2017b`` ``2.4.0`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``2.4.0`` ``-PathCV`` ``intel/2018a`` ``2.4.1`` ``iomkl/2018a`` ``2.4.2`` ``foss/2018b``, ``intel/2018b`` ``2.5.0`` ``intel/2018b`` ``2.5.0`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b`` ``2.5.1`` ``foss/2019a``, ``intel/2018b`` ``2.5.1`` ``-PathCV`` ``intel/2018b`` ``2.5.2`` ``-Python-3.7.2`` ``intel/2019a`` ``2.5.3`` ``-Python-3.7.4`` ``intel/2019b`` ``2.5b`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== ================================================ .. _list_software_PLY_245: *PLY* +++++ PLY is yet another implementation of lex and yacc for Python. *homepage*: http://www.dabeaz.com/ply/ ======== ================= ============== version versionsuffix toolchain ======== ================= ============== ``3.11`` ``-Python-3.6.4`` ``foss/2018a`` ======== ================= ============== .. _list_software_PMIx_350: *PMIx* ++++++ Process Management for Exascale Environments PMI Exascale (PMIx) represents an attempt to provide an extended version of the PMI standard specifically designed to support clusters up to and including exascale sizes. The overall objective of the project is not to branch the existing pseudo-standard definitions - in fact, PMIx fully supports both of the existing PMI-1 and PMI-2 APIs - but rather to (a) augment and extend those APIs to eliminate some current restrictions that impact scalability, and (b) provide a reference implementation of the PMI-server that demonstrates the desired level of scalability. *homepage*: https://pmix.org/ ========= ======================================================= version toolchain ========= ======================================================= ``1.2.5`` ``GCCcore/6.4.0`` ``2.1.3`` ``GCCcore/7.3.0`` ``3.0.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``3.0.2`` ``GCCcore/8.2.0`` ``3.1.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``3.1.4`` ``GCCcore/8.3.0`` ========= ======================================================= .. _list_software_PnetCDF_612: *PnetCDF* +++++++++ Parallel netCDF: A Parallel I/O Library for NetCDF File Access *homepage*: https://trac.mcs.anl.gov/projects/parallel-netcdf ========== =============================== version toolchain ========== =============================== ``1.8.1`` ``intel/2017a`` ``1.9.0`` ``intel/2018a`` ``1.10.0`` ``foss/2018b``, ``intel/2018b`` ========== =============================== .. _list_software_pocl_430: *pocl* ++++++ Pocl is a portable open source (MIT-licensed) implementation of the OpenCL standard *homepage*: http://portablecl.org ======= ================================ version toolchain ======= ================================ ``1.2`` ``GCC/7.3.0-2.30`` ``1.3`` ``GCC/8.2.0-2.31.1`` ``1.4`` ``GCC/8.3.0``, ``gcccuda/2019b`` ======= ================================ .. _list_software_pomkl_547: *pomkl* +++++++ Toolchain with PGI C, C++ and Fortran compilers, alongside Intel MKL & OpenMPI. *homepage*: http://www.pgroup.com/index.htm =========== ========== version toolchain =========== ========== ``2016.03`` ``system`` ``2016.04`` ``system`` ``2016.09`` ``system`` =========== ========== .. _list_software_pompi_549: *pompi* +++++++ Toolchain with PGI C, C++ and Fortran compilers, alongside OpenMPI. *homepage*: http://www.pgroup.com/index.htm =========== ========== version toolchain =========== ========== ``2016.03`` ``system`` ``2016.04`` ``system`` ``2016.09`` ``system`` =========== ========== .. _list_software_poppler_770: *poppler* +++++++++ Poppler is a PDF rendering library based on the xpdf-3.0 code base. *homepage*: https://poppler.freedesktop.org/ ========== ============== version toolchain ========== ============== ``0.70.1`` ``foss/2018b`` ========== ============== .. _list_software_popt_451: *popt* ++++++ Popt is a C library for parsing command line parameters. *homepage*: http://freecode.com/projects/popt ======== ========================= version toolchain ======== ========================= ``1.14`` ``GCC/4.8.2`` ``1.16`` ``GCC/4.9.2``, ``system`` ======== ========================= .. _list_software_Porechop_832: *Porechop* ++++++++++ Porechop is a tool for finding and removing adapters from Oxford Nanopore reads. Adapters on the ends of reads are trimmed off, and when a read has an adapter in its middle, it is treated as chimeric and chopped into separate reads. Porechop performs thorough alignments to effectively find adapters, even at low sequence identity *homepage*: https://github.com/rrwick/Porechop ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``0.2.3`` ``-Python-3.5.2`` ``foss/2016b`` ``0.2.4`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== .. _list_software_poretools_999: *poretools* +++++++++++ A toolkit for working with nanopore sequencing data from Oxford Nanopore. *homepage*: http://poretools.readthedocs.io/en/latest/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.6.0`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============== .. _list_software_Postgres-XL_1064: *Postgres-XL* +++++++++++++ Postgres-XL is a horizontally scalable open source SQL database cluster, flexible enough to handle varying database workloads: *homepage*: http://www.postgres-xl.org ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``9.5r1`` ``-Python-2.7.11`` ``intel/2016a`` ========= ================== =============== .. _list_software_PostgreSQL_980: *PostgreSQL* ++++++++++++ PostgreSQL is a powerful, open source object-relational database system. It is fully ACID compliant, has full support for foreign keys, joins, views, triggers, and stored procedures (in multiple languages). It includes most SQL:2008 data types, including INTEGER, NUMERIC, BOOLEAN, CHAR, VARCHAR, DATE, INTERVAL, and TIMESTAMP. It also supports storage of binary large objects, including pictures, sounds, or video. It has native programming interfaces for C/C++, Java, .Net, Perl, Python, Ruby, Tcl, ODBC, among others, and exceptional documentation. *homepage*: https://www.postgresql.org/ ========= ================== ================================================================ version versionsuffix toolchain ========= ================== ================================================================ ``9.4.7`` ``-Python-2.7.11`` ``intel/2016a`` ``9.5.2`` ``-Python-2.7.11`` ``intel/2016a`` ``9.6.0`` ``-Python-2.7.12`` ``intel/2016b`` ``9.6.2`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``10.2`` ``-Python-2.7.14`` ``intel/2018a`` ``10.3`` ``foss/2018b`` ``10.3`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``11.3`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``11.3`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========= ================== ================================================================ .. _list_software_POT_243: *POT* +++++ POT (Python Optimal Transport) is a Python library provide several solvers for optimization problems related to Optimal Transport for signal, image processing and machine learning. *homepage*: https://github.com/rflamary/POT ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``0.5.1`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================= =============== .. _list_software_POV-Ray_590: *POV-Ray* +++++++++ The Persistence of Vision Raytracer, or POV-Ray, is a ray tracing program which generates images from a text-based scene description, and is available for a variety of computer platforms. POV-Ray is a high-quality, Free Software tool for creating stunning three-dimensional graphics. The source code is available for those wanting to do their own ports. *homepage*: http://www.povray.org/ =========== ================================================================================= version toolchain =========== ================================================================================= ``3.7.0.0`` ``intel/2016b`` ``3.7.0.7`` ``foss/2017b``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` =========== ================================================================================= .. _list_software_PPfold_581: *PPfold* ++++++++ PPfold is a new implementation of pfold, written in Java 6.0. It can predict the consensus secondary structure of RNA alignments through a stochastic context-free grammar coupled to an evolutionary model. It can also use data from chemical probing experiments to predict RNA secondary structure. PPfold is multithreaded, and can solve the structure of much longer alignments than pfold. *homepage*: ihttp://www.daimi.au.dk/~compbio/pfold/downloads.html ========= ================== ========== version versionsuffix toolchain ========= ================== ========== ``3.1.1`` ``-Java-1.8.0_66`` ``system`` ========= ================== ========== .. _list_software_ppl_332: *ppl* +++++ The Parma Polyhedra Library (PPL) provides numerical abstractions especially targeted at applications in the field of analysis and verification of complex systems. *homepage*: https://www.bugseng.com/parma-polyhedra-library ======= ================= version toolchain ======= ================= ``1.2`` ``GCCcore/6.4.0`` ======= ================= .. _list_software_pplacer_743: *pplacer* +++++++++ Pplacer places query sequences on a fixed reference phylogenetic tree to maximize phylogenetic likelihood or posterior probability according to a reference alignment. Pplacer is designed to be fast, to give useful information about uncertainty, and to offer advanced visualization and downstream analysis. *homepage*: http://matsen.fhcrc.org/pplacer/ =============== ========== version toolchain =============== ========== ``1.1.alpha19`` ``system`` =============== ========== .. _list_software_pplpy_565: *pplpy* +++++++ This Python package provides a wrapper to the C++ Parma Polyhedra Library (PPL). *homepage*: https://pypi.org/project/pplpy/ ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``0.8.4`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``0.8.4`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ========= ================== =============================== .. _list_software_PRANK_380: *PRANK* +++++++ PRANK is a probabilistic multiple alignment program for DNA, codon and amino-acid sequences. PRANK is based on a novel algorithm that treats insertions correctly and avoids over-estimation of the number of deletion events. *homepage*: http://wasabiapp.org/software/prank/ ========== =============== version toolchain ========== =============== ``170427`` ``intel/2018a`` ========== =============== .. _list_software_PRC_229: *PRC* +++++ PRC is a stand-alone program for aligning and scoring two profile hidden Markov models. This can be used to detect remote relationships between profiles more effectively than by doing simple profile-sequence comparisons. PRC takes into account all transition and emission probabilities in both hidden Markov models. *homepage*: http//supfam.org/PRC/ ========= =============== version toolchain ========= =============== ``1.5.6`` ``intel/2018a`` ========= =============== .. _list_software_preseq_656: *preseq* ++++++++ Software for predicting library complexity and genome coverage in high-throughput sequencing. *homepage*: http://smithlabresearch.org/software/preseq ========= =============================== version toolchain ========= =============================== ``2.0.2`` ``foss/2016b`` ``2.0.3`` ``foss/2018b``, ``intel/2018a`` ========= =============================== .. _list_software_Primer3_674: *Primer3* +++++++++ Primer3 is a widely used program for designing PCR primers (PCR = 'Polymerase Chain Reaction'). PCR is an essential and ubiquitous tool in genetics and molecular biology. Primer3 can also design hybridization probes and sequencing primers. *homepage*: http://primer3.sourceforge.net ========= ========================================================= version toolchain ========= ========================================================= ``2.3.7`` ``intel/2017b`` ``2.4.0`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ========= ========================================================= .. _list_software_PRINSEQ_546: *PRINSEQ* +++++++++ A bioinformatics tool to PRe-process and show INformation of SEQuence data. *homepage*: http://prinseq.sourceforge.net ========== ================ ============== version versionsuffix toolchain ========== ================ ============== ``0.20.4`` ``-Perl-5.28.0`` ``foss/2018b`` ========== ================ ============== .. _list_software_printproto_1121: *printproto* ++++++++++++ X.org PrintProto protocol headers. *homepage*: http://xorg.freedesktop.org/ ========= =============== version toolchain ========= =============== ``1.0.5`` ``intel/2016a`` ========= =============== .. _list_software_PRISMS-PF_673: *PRISMS-PF* +++++++++++ PRISMS-PF is a powerful, massively parallel finite element code for conducting phase field and other related simulations of microstructural evolution. *homepage*: https://prisms-center.github.io/phaseField ========= =============== version toolchain ========= =============== ``2.1.1`` ``intel/2019a`` ========= =============== .. _list_software_ProbABEL_679: *ProbABEL* ++++++++++ Tool for genome-wide association analysis of imputed genetic data. *homepage*: http://www.genabel.org/packages/ProbABEL ========= ========== version toolchain ========= ========== ``0.5.0`` ``system`` ========= ========== .. _list_software_prodigal_850: *prodigal* ++++++++++ Prodigal (Prokaryotic Dynamic Programming Genefinding Algorithm) is a microbial (bacterial and archaeal) gene finding program developed at Oak Ridge National Laboratory and the University of Tennessee. *homepage*: https://github.com/hyattpd/Prodigal/ ========= ========================================================================== version toolchain ========= ========================================================================== ``2.6.2`` ``GCC/4.9.3-binutils-2.25`` ``2.6.3`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ========================================================================== .. _list_software_PROJ_315: *PROJ* ++++++ Program proj is a standard Unix filter function which converts geographic longitude and latitude coordinates into cartesian coordinates *homepage*: https://proj.org ========= ================================================================================= version toolchain ========= ================================================================================= ``4.9.2`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``4.9.3`` ``foss/2016b``, ``foss/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``5.0.0`` ``foss/2018a``, ``foss/2018b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018a`` ``6.0.0`` ``GCCcore/8.2.0`` ``6.2.1`` ``GCCcore/8.3.0`` ========= ================================================================================= .. _list_software_ProjectQ_808: *ProjectQ* ++++++++++ An open source software framework for quantum computing *homepage*: https://projectq.ch ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``0.4.2`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================= =============== .. _list_software_prokka_648: *prokka* ++++++++ Prokka is a software tool for the rapid annotation of prokaryotic genomes. *homepage*: https://www.vicbioinformatics.com/software.prokka.shtml ========== ================== ================================ version versionsuffix toolchain ========== ================== ================================ ``1.11`` ``-BioPerl-1.7.0`` ``foss/2016b`` ``1.13`` ``-BioPerl-1.7.2`` ``intel/2018a`` ``1.13.4`` ``foss/2018b`` ``1.13.7`` ``gompi/2019a`` ``1.14.5`` ``gompi/2019a``, ``gompi/2019b`` ========== ================== ================================ .. _list_software_prompt-toolkit_1493: *prompt-toolkit* ++++++++++++++++ prompt_toolkit is a Python library for building powerful interactive command lines and terminal applications. *homepage*: https://github.com/jonathanslenders/python-prompt-toolkit ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``1.0.3`` ``-Python-2.7.11`` ``foss/2016a`` ``1.0.3`` ``-Python-3.5.1`` ``foss/2016a`` ``1.0.6`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``1.0.6`` ``-Python-3.5.2`` ``intel/2016b`` ``1.0.13`` ``-Python-2.7.12`` ``intel/2016b`` ========== ================== =============================== .. _list_software_proovread_978: *proovread* +++++++++++ PacBio hybrid error correction through iterative short read consensus *homepage*: https://github.com/BioInf-Wuerzburg/proovread ========== =============== version toolchain ========== =============== ``2.14.1`` ``intel/2017b`` ========== =============== .. _list_software_propy_570: *propy* +++++++ Propy is a protein description software. It allows analyzing sequence-derived structural and physicochemical features, which are very useful in representing and distinguishing proteins or peptides of different structural, functional and interaction properties. These have been widely used in developing methods and software for predicting protein structural and functional classes, protein-protein interactions, drug-target interactions, protein substrates, among others. *homepage*: https://code.google.com/archive/p/protpy ======= ================== ============== version versionsuffix toolchain ======= ================== ============== ``1.0`` ``-Python-2.7.13`` ``foss/2017a`` ======= ================== ============== .. _list_software_Proteinortho_1293: *Proteinortho* ++++++++++++++ Proteinortho is a tool to detect orthologous genes within different species. *homepage*: http://www.bioinf.uni-leipzig.de/Software/proteinortho/ ========= ============================= ============== version versionsuffix toolchain ========= ============================= ============== ``5.16b`` ``-Python-3.6.4-Perl-5.26.1`` ``foss/2018a`` ========= ============================= ============== .. _list_software_protobuf_881: *protobuf* ++++++++++ Google Protocol Buffers *homepage*: https://github.com/google/protobuf/ =========== =================================================== version toolchain =========== =================================================== ``2.5.0`` ``GCCcore/7.3.0``, ``system`` ``2.6.1`` ``system`` ``3.0.2`` ``foss/2016a`` ``3.2.0`` ``foss/2016b``, ``intel/2016b`` ``3.3.0`` ``foss/2016b``, ``intel/2017a`` ``3.4.0`` ``GCCcore/6.4.0``, ``intel/2017a``, ``intel/2017b`` ``3.5.1`` ``intel/2017b`` ``3.6.0`` ``GCCcore/7.3.0`` ``3.6.1`` ``GCCcore/7.3.0`` ``3.6.1.2`` ``GCCcore/8.2.0`` ``3.7.1`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ``3.10.0`` ``GCCcore/8.3.0`` =========== =================================================== .. _list_software_protobuf-python_1600: *protobuf-python* +++++++++++++++++ Python Protocol Buffers runtime library. *homepage*: https://github.com/google/protobuf/ ========= ================== ================================== version versionsuffix toolchain ========= ================== ================================== ``3.0.2`` ``-Python-2.7.11`` ``foss/2016a`` ``3.0.2`` ``-Python-3.5.1`` ``foss/2016a`` ``3.2.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``3.2.0`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` ``3.3.0`` ``-Python-2.7.13`` ``intel/2017a`` ``3.3.0`` ``-Python-3.5.2`` ``foss/2016b`` ``3.3.0`` ``-Python-3.6.1`` ``intel/2017a`` ``3.4.0`` ``-Python-2.7.13`` ``intel/2017a`` ``3.4.0`` ``-Python-2.7.14`` ``intel/2017b`` ``3.4.0`` ``-Python-3.6.1`` ``intel/2017a`` ``3.4.0`` ``-Python-3.6.3`` ``intel/2017b`` ``3.6.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``3.6.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ========= ================== ================================== .. _list_software_pscom_546: *pscom* +++++++ ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer. *homepage*: http://www.par-tec.com ============ ============= version toolchain ============ ============= ``5.0.43`` ``GCC/4.8.2`` ``5.0.44-1`` ``GCC/4.9.2`` ``5.0.48-1`` ``system`` ============ ============= .. _list_software_PSI_236: *PSI* +++++ PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel. *homepage*: http://www.psicode.org/ ================== ===================== =============== version versionsuffix toolchain ================== ===================== =============== ``4.0b6-20160201`` ``-mt-Python-2.7.11`` ``intel/2016a`` ================== ===================== =============== .. _list_software_PSI4_288: *PSI4* ++++++ PSI4 is an open-source suite of ab initio quantum chemistry programs designed for efficient, high-accuracy simulations of a variety of molecular properties. We can routinely perform computations with more than 2500 basis functions running serially or in parallel. *homepage*: http://www.psicode.org/ ========= ========================= =============== version versionsuffix toolchain ========= ========================= =============== ``1.0`` ``-Python-2.7.11`` ``intel/2016a`` ``1.0`` ``-mt-Python-2.7.11`` ``intel/2016a`` ``1.2.1`` ``-Python-2.7.15`` ``intel/2018b`` ``1.2.1`` ``-Python-2.7.15-maxam8`` ``intel/2018b`` ========= ========================= =============== .. _list_software_psmc_435: *psmc* ++++++ This software package infers population size history from a diploid sequence using the Pairwise Sequentially Markovian Coalescent (PSMC) model. *homepage*: https://github.com/lh3/psmc ========= ============================== version toolchain ========= ============================== ``0.6.5`` ``foss/2016a``, ``foss/2018a`` ========= ============================== .. _list_software_psmpi_553: *psmpi* +++++++ ParaStation MPI is an open source high-performance MPI 3.0 implementation, based on MPICH v3. It provides extra low level communication libraries and integration with various batch systems for tighter process control. *homepage*: https://github.com/ParaStation/psmpi2 =========== ============= ============= version versionsuffix toolchain =========== ============= ============= ``5.1.0-1`` ``GCC/4.9.2`` ``5.1.5-1`` ``GCC/4.9.3`` ``5.1.5-1`` ``-mt`` ``GCC/4.9.3`` =========== ============= ============= .. _list_software_psmpi2_603: *psmpi2* ++++++++ ParaStation is a robust and efficient cluster middleware, consisting of a high-performance communication layer (MPI) and a sophisticated management layer. *homepage*: http://www.par-tec.com ========== ============= ============= version versionsuffix toolchain ========== ============= ============= ``5.0.29`` ``GCC/4.8.2`` ``5.0.29`` ``-mt`` ``GCC/4.8.2`` ========== ============= ============= .. _list_software_PSolver_715: *PSolver* +++++++++ Poisson Solver from the BigDFT code compiled as a standalone library. *homepage*: http://bigdft.org/Wiki/index.php?title=BigDFT_website ========= ================================================================================================= version toolchain ========= ================================================================================================= ``1.7.6`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ========= ================================================================================================= .. _list_software_PSORTb_506: *PSORTb* ++++++++ PSORTb v3.0.4 is the most precise bacterial localization prediction tool available. *homepage*: http://psort.org/psortb/index.html ========= ================ ============== version versionsuffix toolchain ========= ================ ============== ``3.0.4`` ``-Perl-5.22.1`` ``foss/2016a`` ========= ================ ============== .. _list_software_psrecord_866: *psrecord* ++++++++++ psrecord is a small utility that uses the psutil library to record the CPU and memory activity of a process. *homepage*: https://github.com/astrofrog/psrecord ======= ================== =============== version versionsuffix toolchain ======= ================== =============== ``1.1`` ``-Python-2.7.14`` ``intel/2018a`` ``1.1`` ``-Python-2.7.15`` ``intel/2018b`` ``1.1`` ``-Python-3.6.4`` ``intel/2018a`` ``1.1`` ``-Python-3.6.6`` ``intel/2018b`` ======= ================== =============== .. _list_software_pstoedit_876: *pstoedit* ++++++++++ pstoedit translates PostScript and PDF graphics into other vector formats *homepage*: http://pstoedit.net/ ======== ==================================== version toolchain ======== ==================================== ``3.70`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ======== ==================================== .. _list_software_psutil_673: *psutil* ++++++++ A cross-platform process and system utilities module for Python *homepage*: https://github.com/giampaolo/psutil ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``4.2.0`` ``-Python-2.7.11`` ``intel/2016a`` ``4.3.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``5.4.3`` ``-Python-2.7.14`` ``intel/2017b`` ``5.4.7`` ``-Python-2.7.15`` ``foss/2018b`` ``5.4.7`` ``-Python-3.6.6`` ``foss/2018b`` ``5.6.1`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``5.6.3`` ``GCCcore/8.2.0`` ========= ================== =============================== .. _list_software_psycopg2_823: *psycopg2* ++++++++++ Psycopg is the most popular PostgreSQL adapter for the Python programming language. *homepage*: http://initd.org/psycopg/ ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``2.7`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``2.8.3`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================== =============================== .. _list_software_ptemcee_739: *ptemcee* +++++++++ ptemcee, pronounced "tem-cee", is fork of Daniel Foreman-Mackey's wonderful emcee to implement parallel tempering more robustly. If you're trying to characterise awkward, multi-model probability distributions, then ptemcee is your friend. *homepage*: https://github.com/willvousden/ptemcee ========= ============== version toolchain ========= ============== ``1.0.0`` ``foss/2019a`` ========= ============== .. _list_software_PTESFinder_916: *PTESFinder* ++++++++++++ Post-Transcriptional Exon Shuffling (PTES) Identification Pipeline *homepage*: https://sourceforge.net/projects/ptesfinder-v1/ ======= =============== version toolchain ======= =============== ``1`` ``intel/2017b`` ======= =============== .. _list_software_pubtcrs_771: *pubtcrs* +++++++++ This repository contains C++ source code for the TCR clustering and correlation analyses described in the manuscript "Human T cell receptor occurrence patterns encode immune history, genetic background, and receptor specificity" by William S DeWitt III, Anajane Smith, Gary Schoch, John A Hansen, Frederick A Matsen IV and Philip Bradley, available on bioRxiv. *homepage*: https://github.com/phbradley/pubtcrs ============ =============== version toolchain ============ =============== ``20180622`` ``intel/2019a`` ============ =============== .. _list_software_pullseq_774: *pullseq* +++++++++ Utility program for extracting sequences from a fasta/fastq file *homepage*: https://github.com/bcthomas/pullseq ========= ================= version toolchain ========= ================= ``1.0.2`` ``GCCcore/7.3.0`` ========= ================= .. _list_software_py_233: *py* ++++ library with cross-python path, ini-parsing, io, code, log facilities *homepage*: http://pylib.readthedocs.org/ ========== ================== ============== version versionsuffix toolchain ========== ================== ============== ``1.4.31`` ``-Python-2.7.11`` ``foss/2016a`` ``1.4.31`` ``-Python-3.5.1`` ``foss/2016a`` ========== ================== ============== .. _list_software_py-cpuinfo_1034: *py-cpuinfo* ++++++++++++ py-cpuinfo gets CPU info with pure Python. *homepage*: https://github.com/workhorsy/py-cpuinfo ========= ========== version toolchain ========= ========== ``5.0.0`` ``system`` ========= ========== .. _list_software_PyAMG_414: *PyAMG* +++++++ PyAMG is a library of Algebraic Multigrid (AMG) solvers with a convenient Python interface. *homepage*: http://pyamg.org ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``3.0.1`` ``-Python-2.7.11`` ``intel/2016a`` ========= ================== =============== .. _list_software_PyAPS3_480: *PyAPS3* ++++++++ Python 3 Atmospheric Phase Screen *homepage*: https://github.com/AngeliqueBenoit/pyaps3 ============ ================= ============== version versionsuffix toolchain ============ ================= ============== ``20190407`` ``-Python-3.7.2`` ``foss/2019a`` ============ ================= ============== .. _list_software_pybedtools_1093: *pybedtools* ++++++++++++ pybedtools wraps and extends BEDTools and offers feature-level manipulations from within Python. *homepage*: https://daler.github.io/pybedtools ========== ================== ================================ version versionsuffix toolchain ========== ================== ================================ ``0.7.10`` ``-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` ``0.7.10`` ``-Python-3.6.6`` ``foss/2018b`` ``0.8.0`` ``foss/2019a``, ``intel/2019a`` ========== ================== ================================ .. _list_software_pyBigWig_802: *pyBigWig* ++++++++++ A python extension, written in C, for quick access to bigBed files and access to and creation of bigWig files. *homepage*: https://github.com/deeptools/pyBigWig ========== ================= ================= version versionsuffix toolchain ========== ================= ================= ``0.3.13`` ``-Python-3.6.6`` ``foss/2018b`` ``0.3.17`` ``GCCcore/8.2.0`` ========== ================= ================= .. _list_software_pybind11_744: *pybind11* ++++++++++ pybind11 is a lightweight header-only library that exposes C++ types in Python and vice versa, mainly to create Python bindings of existing C++ code. *homepage*: https://pybind11.readthedocs.io ========= ================= ================= version versionsuffix toolchain ========= ================= ================= ``2.2.4`` ``-Python-3.6.4`` ``foss/2018a`` ``2.2.4`` ``-Python-3.6.6`` ``intel/2018b`` ``2.4.3`` ``-Python-3.7.4`` ``GCCcore/8.3.0`` ========= ================= ================= .. _list_software_PyCairo_695: *PyCairo* +++++++++ Python bindings for the cairo library *homepage*: https://cairographics.org/pycairo/ ========== ================== ================= version versionsuffix toolchain ========== ================== ================= ``1.10.0`` ``-Python-2.7.11`` ``intel/2016a`` ``1.16.1`` ``-Python-3.6.3`` ``foss/2017b`` ``1.16.2`` ``-Python-2.7.14`` ``intel/2017b`` ``1.18.0`` ``-Python-2.7.14`` ``intel/2018a`` ``1.18.0`` ``-Python-2.7.15`` ``foss/2018b`` ``1.18.0`` ``-Python-3.6.6`` ``foss/2018b`` ``1.18.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================== ================= .. _list_software_PyCharm_692: *PyCharm* +++++++++ PyCharm Community Edition: Python IDE for Professional Developers *homepage*: https://www.jetbrains.com/pycharm/ ============ ========== version toolchain ============ ========== ``2017.2.3`` ``system`` ``2019.3.1`` ``system`` ============ ========== .. _list_software_pycma_538: *pycma* +++++++ A stochastic numerical optimization algorithm for difficult (non-convex, ill-conditioned, multi-modal, rugged, noisy) optimization problems in continuous search spaces, implemented in Python. *homepage*: https://github.com/CMA-ES/pycma ========= =============== version toolchain ========= =============== ``2.7.0`` ``intel/2019a`` ========= =============== .. _list_software_PyCogent_809: *PyCogent* ++++++++++ PyCogent is a software library for genomic biology. It is a fully integrated and thoroughly tested framework for: controlling third-party applications; devising workflows; querying databases; conducting novel probabilistic analyses of biological sequence evolution; and generating publication quality graphics. *homepage*: http://pycogent.org ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``1.5.3`` ``-Python-2.7.12`` ``intel/2016b`` ``1.9`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``1.9`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== =============================== .. _list_software_PyCUDA_486: *PyCUDA* ++++++++ PyCUDA lets you access Nvidia’s CUDA parallel computation API from Python. *homepage*: http://mathema.tician.de/software/pycuda ============ ============================= =============== version versionsuffix toolchain ============ ============================= =============== ``2016.1.2`` ``-Python-2.7.12`` ``intel/2016b`` ``2017.1.1`` ``-Python-2.7.14`` ``intel/2018a`` ``2018.1`` ``-Python-3.6.4-CUDA-9.1.85`` ``intel/2018a`` ============ ============================= =============== .. _list_software_PyDatastream_1231: *PyDatastream* ++++++++++++++ Lightweight SOAP client *homepage*: https://pypi.python.org/pypi/suds-py3 ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``0.5.1`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================= =============== .. _list_software_pydicom_757: *pydicom* +++++++++ Pure python package for DICOM medical file reading and writing. *homepage*: https://github.com/pydicom/pydicom ========= ================== ================= version versionsuffix toolchain ========= ================== ================= ``0.9.9`` ``-Python-2.7.11`` ``intel/2016a`` ``1.2.2`` ``GCCcore/8.2.0`` ========= ================== ================= .. _list_software_pydlpoly_893: *pydlpoly* ++++++++++ Pydlpoly is a molecular dynamics simulation package which is a modified version of DL-POLY with a Python language interface. *homepage*: http://cmc.aci.ruhr-uni-bochum.de/cmc/ ============ ================== =============== version versionsuffix toolchain ============ ================== =============== ``20150225`` ``-Python-2.7.12`` ``intel/2016b`` ``20150225`` ``-Python-2.7.13`` ``intel/2017a`` ============ ================== =============== .. _list_software_pyEGA3_489: *pyEGA3* ++++++++ A basic Python-based EGA download client *homepage*: https://github.com/EGA-archive/ega-download-client ========== ================= ================= version versionsuffix toolchain ========== ================= ================= ``3.0.33`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================= ================= .. _list_software_pyenchant_970: *pyenchant* +++++++++++ PyEnchant is a spellchecking library for Python, based on the excellent Enchant library. *homepage*: https://pythonhosted.org/pyenchant/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.6.8`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== .. _list_software_PyFFmpeg_766: *PyFFmpeg* ++++++++++ Python FFmpeg wrapper *homepage*: https://github.com/mhaller/pyffmpeg =========== ================== ================ version versionsuffix toolchain =========== ================== ================ ``2.1beta`` ``-Python-2.7.10`` ``gimkl/2.11.5`` ``2.1beta`` ``-Python-2.7.11`` ``intel/2016a`` =========== ================== ================ .. _list_software_pyFFTW_544: *pyFFTW* ++++++++ A pythonic wrapper around FFTW, the FFT library, presenting a unified interface for all the supported transforms. *homepage*: https://github.com/pyFFTW/pyFFTW ========== =============== version toolchain ========== =============== ``0.11.1`` ``intel/2019a`` ========== =============== .. _list_software_pyfits_671: *pyfits* ++++++++ The PyFITS module is a Python library providing access to FITS (Flexible Image Transport System) *homepage*: https://pythonhosted.org/pyfits/ ======= ================== =============== version versionsuffix toolchain ======= ================== =============== ``3.5`` ``-Python-2.7.15`` ``intel/2018b`` ======= ================== =============== .. _list_software_PyFMI_421: *PyFMI* +++++++ PyFMI is a package for loading and interacting with Functional Mock-Up Units (FMUs), which are compiled dynamic models compliant with the Functional Mock-Up Interface (FMI) *homepage*: https://pypi.org/project/PyFMI/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``2.4.0`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============== .. _list_software_PyFR_353: *PyFR* ++++++ PyFR is an open-source Python based framework for solving advection-diffusion type problems on streaming architectures using the Flux Reconstruction approach of Huynh. The framework is designed to solve a range of governing systems on mixed unstructured grids containing various element types. It is also designed to target a range of hardware platforms via use of an in-built domain specific language derived from the Mako templating engine. *homepage*: http://http://www.pyfr.org ========= ============================= =============== version versionsuffix toolchain ========= ============================= =============== ``1.7.6`` ``-Python-3.6.4-CUDA-9.1.85`` ``intel/2018a`` ========= ============================= =============== .. _list_software_pygccxml_871: *pygccxml* ++++++++++ Python package for easy C++ declarations navigation. *homepage*: https://pypi.python.org/pypi/pygccxml ============ ================== ============== version versionsuffix toolchain ============ ================== ============== ``20160706`` ``-Python-2.7.11`` ``foss/2016a`` ``20160706`` ``-Python-3.5.1`` ``foss/2016a`` ============ ================== ============== .. _list_software_pyGIMLi_635: *pyGIMLi* +++++++++ pyGIMLi is an open-source multi-method library for solving inverse and forward tasks related to geophysical problems. Written in C++ and Python, it offers both efficiency and flexibility allowing you to quickly build your own robust inversion applications for the geophysical problem at hand. *homepage*: http://www.pygimli.org/ ============ ================== ============== version versionsuffix toolchain ============ ================== ============== ``20160803`` ``-Python-2.7.11`` ``foss/2016a`` ``20160803`` ``-Python-3.5.1`` ``foss/2016a`` ============ ================== ============== .. _list_software_Pygments_855: *Pygments* ++++++++++ Generic syntax highlighter suitable for use in code hosting, forums, wikis or other applications that need to prettify source code. *homepage*: http://pygments.org/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.1.3`` ``-Python-2.7.11`` ``foss/2016a`` ``2.1.3`` ``-Python-3.5.1`` ``foss/2016a`` ========= ================== ============== .. _list_software_PyGObject_871: *PyGObject* +++++++++++ Python Bindings for GLib/GObject/GIO/GTK+ *homepage*: http://www.pygtk.org/ ========== ================== ================= version versionsuffix toolchain ========== ================== ================= ``2.28.6`` ``-Python-2.7.11`` ``intel/2016a`` ``2.28.6`` ``-Python-2.7.14`` ``intel/2017b`` ``2.28.7`` ``-Python-2.7.14`` ``intel/2018a`` ``2.28.7`` ``-Python-2.7.15`` ``foss/2018b`` ``3.34.0`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================== ================= .. _list_software_pygrib_653: *pygrib* ++++++++ Python interface for reading and writing GRIB data *homepage*: https://jswhit.github.io/pygrib ========= ============== version toolchain ========= ============== ``2.0.4`` ``foss/2019a`` ========= ============== .. _list_software_PyGTK_431: *PyGTK* +++++++ PyGTK lets you to easily create programs with a graphical user interface using the Python programming language. *homepage*: http://www.pygtk.org/ ========== ================== ================================ version versionsuffix toolchain ========== ================== ================================ ``2.24.0`` ``-Python-2.7.11`` ``intel/2016a`` ``2.24.0`` ``-Python-2.7.14`` ``intel/2017b``, ``intel/2018a`` ``2.24.0`` ``-Python-2.7.15`` ``foss/2018b`` ========== ================== ================================ .. _list_software_PyGTS_439: *PyGTS* +++++++ PyGTS is a python package used to construct, manipulate, and perform computations on triangulated surfaces. It is a hand-crafted and pythonic binding for the GNU Triangulated Surface (GTS) Library. *homepage*: https://sourceforge.net/projects/pygts/ ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``0.3.1`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``0.3.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``0.3.1`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============================== .. _list_software_PyGWAS_507: *PyGWAS* ++++++++ PyGWAS is a library for running Genome Wide Association studies. *homepage*: https://github.com/timeu/pygwas ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``1.2.0`` ``-Python-2.7.11`` ``foss/2016a`` ``1.3.1`` ``-Python-2.7.11`` ``foss/2016a`` ``1.4.0`` ``-Python-2.7.11`` ``foss/2016a`` ``1.5.0`` ``-Python-2.7.11`` ``foss/2016a`` ``1.6.1`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``1.7.1`` ``-Python-2.7.13`` ``foss/2017a`` ========= ================== =============================== .. _list_software_pyhdf_539: *pyhdf* +++++++ Python wrapper around the NCSA HDF version 4 library *homepage*: https://github.com/fhs/pyhdf ========== ============== version toolchain ========== ============== ``0.10.1`` ``foss/2019a`` ========== ============== .. _list_software_pyiron_673: *pyiron* ++++++++ An integrated development environment (IDE) for computational materials science. *homepage*: https://github.com/pyiron/pyiron ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``0.2.5`` ``-Python-3.7.2`` ``intel/2019a`` ========= ================= =============== .. _list_software_Pyke3_460: *Pyke3* +++++++ Pyke introduces a form of Logic Programming (inspired by Prolog) to the Python community by providing a knowledge-based inference engine (expert system) written in 100% Python. *homepage*: http://sourceforge.net/projects/pyke/ ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``1.1.1`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================= =============== .. _list_software_Pylint_640: *Pylint* ++++++++ Pylint is a tool that checks for errors in Python code, tries to enforce a coding standard and looks for code smells. It can also look for certain type errors, it can recommend suggestions about how particular blocks can be refactored and can offer you details about the code's complexity. *homepage*: https://www.pylint.org/ ========= ================== ================================================ version versionsuffix toolchain ========= ================== ================================================ ``1.9.3`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` ========= ================== ================================================ .. _list_software_pymatgen_869: *pymatgen* ++++++++++ Python Materials Genomics is a robust materials analysis code that defines core object representations for structures and molecules with support for many electronic structure codes. *homepage*: https://pypi.python.org/pypi/pymatgen ============== ================== ========================= version versionsuffix toolchain ============== ================== ========================= ``3.5.0`` ``-Python-2.7.11`` ``intel/2016.02-GCC-4.9`` ``4.1.1`` ``-Python-2.7.12`` ``intel/2016b`` ``4.3.2`` ``-Python-2.7.12`` ``intel/2016b`` ``4.7.3`` ``-Python-2.7.13`` ``intel/2017a`` ``2017.10.16`` ``-Python-2.7.14`` ``intel/2017b`` ``2017.10.16`` ``-Python-3.6.3`` ``intel/2017b`` ============== ================== ========================= .. _list_software_pymatgen-db_1112: *pymatgen-db* +++++++++++++ Pymatgen-db is a database add-on for the Python Materials Genomics (pymatgen) materials analysis library. *homepage*: https://pypi.python.org/pypi/pymatgen-db ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.6.5`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== .. _list_software_pymbar_651: *pymbar* ++++++++ The pymbar package contains the pymbar suite of tools for the analysis of simulated and experimental data with the multistate Bennett acceptance ratio (MBAR) estimator. *homepage*: http://pymbar.readthedocs.io/en/master/ ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``3.0.3`` ``-Python-3.6.3`` ``intel/2017b`` ========= ================= =============== .. _list_software_pymemcache_1052: *pymemcache* ++++++++++++ A comprehensive, fast, pure-Python memcached client. *homepage*: https://github.com/pinterest/pymemcache ========= ================= =============================== version versionsuffix toolchain ========= ================= =============================== ``2.1.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ========= ================= =============================== .. _list_software_PyNAST_511: *PyNAST* ++++++++ PyNAST is a reimplementation of the NAST sequence aligner, which has become a popular tool for adding new 16s rRNA sequences to existing 16s rRNA alignments. This reimplementation is more flexible, faster, and easier to install and maintain than the original NAST implementation. *homepage*: https://biocore.github.io/pynast ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``1.2.2`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``1.2.2`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== =============================== .. _list_software_Pyomo_532: *Pyomo* +++++++ Pyomo is a Python-based open-source software package that supports a diverse set of optimization capabilities for formulating and analyzing optimization models. *homepage*: http://www.pyomo.org/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``5.5.0`` ``-Python-2.7.15`` ``foss/2018b`` ``5.5.0`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================== ============== .. _list_software_PyOpenGL_750: *PyOpenGL* ++++++++++ PyOpenGL is the most common cross platform Python binding to OpenGL and related APIs. *homepage*: http://pyopengl.sourceforge.net =========== ================== =============================== version versionsuffix toolchain =========== ================== =============================== ``3.1.1a1`` ``GCCcore/8.2.0`` ``3.1.1a1`` ``-Python-2.7.11`` ``intel/2016a`` ``3.1.1a1`` ``-Python-2.7.12`` ``foss/2016b`` ``3.1.1a1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b`` ``3.1.3b2`` ``-Python-2.7.14`` ``intel/2018a`` ``3.1.3b2`` ``-Python-2.7.15`` ``foss/2018b`` =========== ================== =============================== .. _list_software_pyplusplus_1137: *pyplusplus* ++++++++++++ Py++ is a code generator for Boost.Python that simplifies writing Python bindings of a C/C++ library The tool is implemented as a Python module which is controlled by a user script. *homepage*: https://bitbucket.org/ompl/pyplusplus ============ ================== ============== version versionsuffix toolchain ============ ================== ============== ``20160707`` ``-Python-2.7.11`` ``foss/2016a`` ``20160707`` ``-Python-3.5.1`` ``foss/2016a`` ============ ================== ============== .. _list_software_pyproj_676: *pyproj* ++++++++ Python interface to PROJ4 library for cartographic transformations *homepage*: https://pyproj4.github.io/pyproj ========= ================= version toolchain ========= ================= ``2.1.3`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_pyqstem_787: *pyqstem* +++++++++ QSTEM is a program for quantitative image simulation in electron microscopy, including TEM, STEM and CBED image simulation. This project interfaces the QSTEM code with Python and the Atomic Simulation Environment (ASE) to provide a single environment for building models, simulating and analysing images. *homepage*: https://github.com/jacobjma/PyQSTEM ========= ================= =============================== version versionsuffix toolchain ========= ================= =============================== ``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ========= ================= =============================== .. _list_software_PyQt_398: *PyQt* ++++++ PyQt is a set of Python v2 and v3 bindings for Digia's Qt application framework. *homepage*: http://www.riverbankcomputing.co.uk/software/pyqt ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``4.11.4`` ``-Python-2.7.11`` ``intel/2016a`` ``4.11.4`` ``-Python-2.7.12`` ``intel/2016b`` ``4.12`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``4.12`` ``-Python-2.7.13`` ``intel/2017a`` ``4.12.1`` ``-Python-2.7.14`` ``foss/2018a`` ``4.12.3`` ``-Python-2.7.15`` ``fosscuda/2018b`` ========== ================== =============================== .. _list_software_PyQt5_451: *PyQt5* +++++++ PyQt5 is a set of Python bindings for v5 of the Qt application framework from The Qt Company. *homepage*: http://www.riverbankcomputing.co.uk/software/pyqt ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``5.7`` ``-Python-2.7.11`` ``foss/2016a`` ``5.7.1`` ``-Python-2.7.12`` ``intel/2016b`` ``5.8.2`` ``-Python-2.7.13`` ``intel/2017a`` ``5.9.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``5.9.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``5.11.3`` ``-Python-3.6.6`` ``foss/2018b`` ``5.12.1`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``5.12.1`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================== =============================== .. _list_software_PyQtGraph_896: *PyQtGraph* +++++++++++ PyQtGraph is a pure-python graphics and GUI library built on PyQt4/PySide and numpy. *homepage*: http://www.pyqtgraph.org/ ========== ================= =============== version versionsuffix toolchain ========== ================= =============== ``0.10.0`` ``-Python-3.6.4`` ``intel/2018a`` ``0.10.0`` ``-Python-3.7.2`` ``intel/2019a`` ========== ================= =============== .. _list_software_PyRETIS_592: *PyRETIS* +++++++++ PyRETIS is a Python library for rare event molecular simulations with emphasis on methods based on transition interface sampling and replica exchange transition interface sampling. *homepage*: http://www.pyretis.org ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``2.1.0`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================= =============== .. _list_software_pyringe_766: *pyringe* +++++++++ Debugger capable of attaching to and injecting code into python processes. *homepage*: https://github.com/google/pyringe ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.0.2`` ``-Python-2.7.11`` ``intel/2016a`` ========= ================== =============== .. _list_software_Pyro4_478: *Pyro4* +++++++ Pyro means PYthon Remote Objects. It is a library that enables you to build applications in which objects can talk to eachother over the network, with minimal programming effort. *homepage*: https://pypi.python.org/pypi/Pyro4 ======== ================== ============== version versionsuffix toolchain ======== ================== ============== ``4.47`` ``-Python-2.7.11`` ``foss/2016a`` ======== ================== ============== .. _list_software_Pysam_522: *Pysam* +++++++ Pysam is a python module for reading and manipulating Samfiles. It's a lightweight wrapper of the samtools C-API. Pysam also includes an interface for tabix. *homepage*: https://github.com/pysam-developers/pysam ============ ================== ============================================================== version versionsuffix toolchain ============ ================== ============================================================== ``0.8.4`` ``-Python-2.7.12`` ``intel/2016b`` ``0.9.1.4`` ``-Python-2.7.12`` ``foss/2016b`` ``0.10.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``0.12.0.1`` ``-Python-2.7.13`` ``intel/2017a`` ``0.12.0.1`` ``-Python-2.7.14`` ``intel/2017b`` ``0.12.0.1`` ``-Python-3.6.3`` ``intel/2017b`` ``0.13`` ``-Python-2.7.14`` ``intel/2017b`` ``0.13.0`` ``-Python-3.6.3`` ``intel/2017b`` ``0.14`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``0.14`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``0.14`` ``-Python-3.6.4`` ``intel/2018a`` ``0.14.1`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``0.14.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``0.15.1`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``0.15.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``0.15.2`` ``GCC/8.2.0-2.31.1``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ``0.15.3`` ``GCC/8.3.0``, ``iccifort/2019.5.281`` ============ ================== ============================================================== .. _list_software_pyScaf_614: *pyScaf* ++++++++ pyScaf orders contigs from genome assemblies utilising several types of information *homepage*: https://github.com/lpryszcz/pyScaf ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``0.12a4`` ``-Python-2.7.14`` ``intel/2017b`` ========== ================== =============== .. _list_software_PySCF_421: *PySCF* +++++++ PySCF is an open-source collection of electronic structure modules powered by Python. *homepage*: http://www.pyscf.org ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``1.6.3`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================= ============== .. _list_software_pyshp_564: *pyshp* +++++++ Pure Python read/write support for ESRI Shapefile format *homepage*: https://github.com/GeospatialPython/pyshp ========== ================= ============== version versionsuffix toolchain ========== ================= ============== ``1.2.12`` ``-Python-3.6.2`` ``foss/2017b`` ========== ================= ============== .. _list_software_Pysolar_746: *Pysolar* +++++++++ Pysolar is a collection of Python libraries for simulating the irradiation of any point on earth by the sun. *homepage*: http://pysolar.org/ ======= ================= ================= version versionsuffix toolchain ======= ================= ================= ``0.7`` ``-Python-3.6.3`` ``intel/2017b`` ``0.7`` ``-Python-3.6.4`` ``intel/2018a`` ``0.8`` ``-Python-3.6.6`` ``intel/2018b`` ``0.8`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ======= ================= ================= .. _list_software_pysqlite_891: *pysqlite* ++++++++++ pysqlite is an interface to the SQLite 3.x embedded relational database engine. It is almost fully compliant with the Python database API version 2.0 also exposes the unique features of SQLite. *homepage*: https://pypi.python.org/pypi/pysqlite ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.8.2`` ``-Python-2.7.11`` ``foss/2016a`` ========= ================== ============== .. _list_software_PyStan_607: *PyStan* ++++++++ Python interface to Stan, a package for Bayesian inference using the No-U-Turn sampler, a variant of Hamiltonian Monte Carlo. *homepage*: https://github.com/stan-dev/pystan ============ ================= =============== version versionsuffix toolchain ============ ================= =============== ``2.19.0.0`` ``-Python-3.6.4`` ``intel/2018a`` ============ ================= =============== .. _list_software_pystran_785: *pystran* +++++++++ Toolset of dynamical model STRucture ANalysis algorithms *homepage*: http://stijnvanhoey.github.io/pystran/ ============== ================== =============== version versionsuffix toolchain ============== ================== =============== ``2017.04.20`` ``-Python-2.7.14`` ``intel/2017b`` ============== ================== =============== .. _list_software_PyTables_804: *PyTables* ++++++++++ PyTables is a package for managing hierarchical datasets and designed to efficiently and easily cope with extremely large amounts of data. PyTables is built on top of the HDF5 library, using the Python language and the NumPy package. It features an object-oriented interface that, combined with C extensions for the performance-critical parts of the code (generated using Cython), makes it a fast, yet extremely easy to use tool for interactively browse, process and search very large amounts of data. One important feature of PyTables is that it optimizes memory and disk resources so that data takes much less space (specially if on-flight compression is used) than other solutions such as relational or object oriented databases. *homepage*: http://www.pytables.org =========== ================== ================================== version versionsuffix toolchain =========== ================== ================================== ``3.2.2`` ``-Python-2.7.12`` ``foss/2016b`` ``3.2.3.1`` ``-Python-2.7.12`` ``intel/2016b`` ``3.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``3.3.0`` ``-Python-3.5.2`` ``intel/2016b`` ``3.4.2`` ``-Python-2.7.13`` ``foss/2017a`` ``3.4.2`` ``-Python-3.6.1`` ``intel/2017a`` ``3.4.2`` ``-Python-3.6.3`` ``intel/2017b`` ``3.4.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``3.4.4`` ``-Python-2.7.15`` ``foss/2018b`` ``3.4.4`` ``-Python-3.5.1`` ``foss/2016a`` ``3.4.4`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``3.5.2`` ``intel/2019a`` ``3.5.2`` ``-Python-2.7.14`` ``intel/2018a`` =========== ================== ================================== .. _list_software_pytest_681: *pytest* ++++++++ pytest: simple powerful testing with Python *homepage*: http://pytest.org ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``3.0.1`` ``-Python-2.7.11`` ``foss/2016a`` ``3.0.1`` ``-Python-3.5.1`` ``foss/2016a`` ``3.8.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``3.8.2`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``3.8.2`` ``-Python-2.7.15`` ``intel/2018b`` ``3.8.2`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``3.8.2`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``4.3.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``4.4.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``4.4.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ========= ================== =============================== .. _list_software_PYTHIA_463: *PYTHIA* ++++++++ PYTHIA is a standard tool for the generation of events in high-energy collisions, comprising a coherent set of physics models for the evolution from a few-body hard process to a complex multiparticle final state. *homepage*: http://home.thep.lu.se/~torbjorn/Pythia.html ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``8.226`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== .. _list_software_Python_642: *Python* ++++++++ Python is a programming language that lets you work more quickly and integrate your systems more effectively. *homepage*: https://python.org/ ========== ================= ================================================================================================================================================================= version versionsuffix toolchain ========== ================= ================================================================================================================================================================= ``2.7.9`` ``-bare`` ``GCC/4.8.4``, ``GCC/4.9.2`` ``2.7.10`` ``gimkl/2.11.5`` ``2.7.10`` ``-bare`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25`` ``2.7.11`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``2.7.11`` ``-bare`` ``GCC/4.9.3-2.25`` ``2.7.11`` ``-libX11-1.6.3`` ``intel/2016a`` ``2.7.12`` ``foss/2016b``, ``intel/2016b``, ``iomkl/2017a`` ``2.7.12`` ``-bare`` ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` ``2.7.13`` ``foss/2017a``, ``intel/2017a`` ``2.7.13`` ``-bare`` ``GCCcore/6.3.0`` ``2.7.14`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``intel/2017b``, ``intel/2018.01``, ``intel/2018a``, ``intelcuda/2017b``, ``iomkl/2018a`` ``2.7.14`` ``-bare`` ``GCCcore/6.4.0`` ``2.7.15`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``2.7.15`` ``-bare`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``2.7.16`` ``GCCcore/8.3.0`` ``3.5.1`` ``foss/2016a``, ``intel/2016a`` ``3.5.2`` ``foss/2016.04``, ``foss/2016b``, ``intel/2016b`` ``3.5.2`` ``-bare`` ``GCC/5.4.0-2.26``, ``iccifort/2016.3.210-GCC-5.4.0-2.26`` ``3.6.1`` ``foss/2017a``, ``intel/2017a`` ``3.6.2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.00`` ``3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018.01``, ``intelcuda/2017b`` ``3.6.4`` ``foss/2017a``, ``foss/2018a``, ``fosscuda/2018a``, ``golf/2018a``, ``intel/2018a``, ``iomkl/2018.02``, ``iomkl/2018a`` ``3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.7.0`` ``foss/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.7.2`` ``GCCcore/8.2.0`` ``3.7.4`` ``GCCcore/8.3.0`` ========== ================= ================================================================================================================================================================= .. _list_software_python-igraph_1354: *python-igraph* +++++++++++++++ Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis. *homepage*: http://igraph.org/python =============== ================== =============== version versionsuffix toolchain =============== ================== =============== ``0.7.1.post6`` ``-Python-2.7.14`` ``intel/2017b`` ``0.7.1.post6`` ``-Python-3.6.6`` ``foss/2018b`` =============== ================== =============== .. _list_software_python-Levenshtein_1876: *python-Levenshtein* ++++++++++++++++++++ Python extension for computing string edit distances and similarities. *homepage*: https://pypi.org/project/python-Levenshtein/ ========== ================= ============== version versionsuffix toolchain ========== ================= ============== ``0.12.0`` ``-Python-3.6.6`` ``foss/2018b`` ========== ================= ============== .. _list_software_python-parasail_1564: *python-parasail* +++++++++++++++++ This package contains Python bindings for parasail. *homepage*: https://pypi.org/project/parasail/ ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``1.1.12`` ``-Python-2.7.14`` ``intel/2018a`` ``1.1.16`` ``-Python-3.6.6`` ``foss/2018b`` ========== ================== =============== .. _list_software_pythran_774: *pythran* +++++++++ Pythran is an ahead of time compiler for a subset of the Python language, with a focus on scientific computing. It takes a Python module annotated with a few interface description and turns it into a native Python module with the same interface, but (hopefully) faster. *homepage*: https://pythran.readthedocs.io =============== ================= ============== version versionsuffix toolchain =============== ================= ============== ``0.9.4.post1`` ``-Python-3.7.4`` ``foss/2019b`` =============== ================= ============== .. _list_software_PyTorch_713: *PyTorch* +++++++++ Tensors and Dynamic neural networks in Python with strong GPU acceleration. PyTorch is a deep learning framework that puts Python first. *homepage*: https://pytorch.org/ ========= ============================= ================================== version versionsuffix toolchain ========= ============================= ================================== ``0.3.1`` ``-Python-2.7.14`` ``fosscuda/2017b`` ``0.3.1`` ``-Python-3.6.3`` ``fosscuda/2017b`` ``0.3.1`` ``-Python-3.6.4`` ``intel/2018a`` ``0.3.1`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` ``0.4.1`` ``-Python-3.6.4`` ``intel/2018a`` ``1.0.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``1.1.0`` ``-Python-3.7.2`` ``foss/2019a`` ``1.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``1.3.1`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ========= ============================= ================================== .. _list_software_PyYAML_508: *PyYAML* ++++++++ PyYAML is a YAML parser and emitter for the Python programming language. *homepage*: https://github.com/yaml/pyyaml ========= ================== ==================================================================================== version versionsuffix toolchain ========= ================== ==================================================================================== ``3.11`` ``-Python-2.7.11`` ``intel/2016a`` ``3.12`` ``system`` ``3.12`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``3.12`` ``-Python-2.7.13`` ``intel/2017a`` ``3.12`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018a`` ``3.12`` ``-Python-3.5.2`` ``intel/2016b`` ``3.12`` ``-Python-3.6.1`` ``intel/2017a`` ``3.12`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b`` ``3.12`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``3.13`` ``system`` ``3.13`` ``-Python-2.7.15`` ``fosscuda/2018b``, ``intel/2018b`` ``3.13`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``5.1`` ``GCCcore/8.2.0`` ``5.1.2`` ``GCCcore/8.3.0`` ========= ================== ==================================================================================== .. _list_software_PyZMQ_449: *PyZMQ* +++++++ Python bindings for ZeroMQ *homepage*: http://www.zeromq.org/bindings:python ========== ======================= =============================== version versionsuffix toolchain ========== ======================= =============================== ``15.2.0`` ``-Python-2.7.11-zmq4`` ``foss/2016a``, ``intel/2016a`` ``15.2.0`` ``-Python-3.5.1-zmq4`` ``intel/2016a`` ``15.3.0`` ``-Python-2.7.11-zmq4`` ``foss/2016a`` ``15.3.0`` ``-Python-3.5.1-zmq4`` ``foss/2016a`` ``15.4.0`` ``-Python-2.7.12-zmq4`` ``intel/2016b`` ``15.4.0`` ``-Python-3.5.2-zmq4`` ``intel/2016b`` ``16.0.2`` ``-Python-2.7.12-zmq4`` ``foss/2016b``, ``intel/2016b`` ``16.0.2`` ``-Python-2.7.13-zmq4`` ``foss/2017a``, ``intel/2017a`` ``16.0.2`` ``-Python-3.5.2-zmq4`` ``foss/2016b``, ``intel/2016b`` ``16.0.3`` ``-Python-2.7.14-zmq4`` ``intel/2017b`` ``17.0.0`` ``-Python-2.7.14-zmq4`` ``foss/2018a`` ``17.0.0`` ``-Python-3.6.4-zmq4`` ``foss/2018a`` ========== ======================= =============================== .. _list_software_letter_q: *Q* --- :ref:`list_software_Q6_135` - :ref:`list_software_QCA_213` - :ref:`list_software_qcint_543` - :ref:`list_software_QDD_217` - :ref:`list_software_QEMU_312` - :ref:`list_software_QGIS_308` - :ref:`list_software_Qhull_518` - :ref:`list_software_QIIME_373` - :ref:`list_software_QIIME2_423` - :ref:`list_software_Qiskit_629` - :ref:`list_software_QJson_491` - :ref:`list_software_QML_234` - :ref:`list_software_qpth_445` - :ref:`list_software_qrupdate_870` - :ref:`list_software_QScintilla_1012` - :ref:`list_software_Qt_197` - :ref:`list_software_Qt5_250` - :ref:`list_software_Qt5Webkit_864` - :ref:`list_software_QtKeychain_1009` - :ref:`list_software_QTLtools_802` - :ref:`list_software_qtop_452` - :ref:`list_software_Qualimap_826` - :ref:`list_software_Quandl_613` - :ref:`list_software_QuantumESPRESSO_1375` - :ref:`list_software_QUAST_398` - :ref:`list_software_QuaZIP_538` - :ref:`list_software_QuickFF_649` - :ref:`list_software_Quip_415` - :ref:`list_software_Quorum_649` - :ref:`list_software_QuTiP_467` - :ref:`list_software_Qwt_316` - :ref:`list_software_QwtPolar_826` .. _list_software_Q6_135: *Q6* ++++ EVB, FEP and LIE simulator. *homepage*: https://github.com/qusers/Q6 ============ =============== version toolchain ============ =============== ``20180205`` ``gompi/2019a`` ============ =============== .. _list_software_QCA_213: *QCA* +++++ Taking a hint from the similarly-named Java Cryptography Architecture, QCA aims to provide a straightforward and cross-platform crypto API, using Qt datatypes and conventions. QCA separates the API from the implementation, using plugins known as Providers. The advantage of this model is to allow applications to avoid linking to or explicitly depending on any particular cryptographic library. This allows one to easily change or upgrade crypto implementations without even needing to recompile the application! QCA should work everywhere Qt does, including Windows/Unix/MacOSX. *homepage*: http://delta.affinix.com/qca/ ========= ================================================== version toolchain ========= ================================================== ``2.1.0`` ``foss/2016a``, ``intel/2016b`` ``2.1.3`` ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b`` ========= ================================================== .. _list_software_qcint_543: *qcint* +++++++ libcint is an open source library for analytical Gaussian integrals. qcint is an optimized libcint branch for the x86-64 platform. *homepage*: http://wiki.sunqm.net/libcint ========== ============== version toolchain ========== ============== ``3.0.18`` ``foss/2019a`` ========== ============== .. _list_software_QDD_217: *QDD* +++++ A user-friendly program to select microsatellite markers and design primers from large sequencing projects. *homepage*: http://net.imbe.fr/~emeglecz/qdd.html ========= ================ =============== version versionsuffix toolchain ========= ================ =============== ``3.1.2`` ``-Perl-5.28.0`` ``intel/2018b`` ========= ================ =============== .. _list_software_QEMU_312: *QEMU* ++++++ QEMU is a generic and open source machine emulator and virtualizer. *homepage*: https://www.qemu.org/ ========== =============== version toolchain ========== =============== ``2.10.1`` ``intel/2017b`` ========== =============== .. _list_software_QGIS_308: *QGIS* ++++++ QGIS is a user friendly Open Source Geographic Information System (GIS) *homepage*: http://www.qgis.org/ =========== ================== =============== version versionsuffix toolchain =========== ================== =============== ``2.14.12`` ``-Python-2.7.12`` ``intel/2016b`` ``2.18.4`` ``-Python-2.7.12`` ``foss/2016b`` ``3.4.12`` ``-Python-3.7.2`` ``foss/2019a`` =========== ================== =============== .. _list_software_Qhull_518: *Qhull* +++++++ Qhull computes the convex hull, Delaunay triangulation, Voronoi diagram, halfspace intersection about a point, furthest-site Delaunay triangulation, and furthest-site Voronoi diagram. The source code runs in 2-d, 3-d, 4-d, and higher dimensions. Qhull implements the Quickhull algorithm for computing the convex hull. *homepage*: http://www.qhull.org ========== ============================================================================================================================================================================= version toolchain ========== ============================================================================================================================================================================= ``2015.2`` ``GCCcore/5.4.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ========== ============================================================================================================================================================================= .. _list_software_QIIME_373: *QIIME* +++++++ QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. *homepage*: http://qiime.org/ ========= ========== version toolchain ========= ========== ``1.9.1`` ``system`` ========= ========== .. _list_software_QIIME2_423: *QIIME2* ++++++++ QIIME is an open-source bioinformatics pipeline for performing microbiome analysis from raw DNA sequencing data. *homepage*: http://qiime2.org/ =========== ========== version toolchain =========== ========== ``2017.10`` ``system`` ``2018.2`` ``system`` ``2019.4`` ``system`` ``2019.7`` ``system`` =========== ========== .. _list_software_Qiskit_629: *Qiskit* ++++++++ Qiskit is an open-source framework for working with noisy quantum computers at the level of pulses, circuits, and algorithms. *homepage*: https://qiskit.org ========== ================= ============== version versionsuffix toolchain ========== ================= ============== ``0.11.1`` ``-Python-3.7.2`` ``foss/2019a`` ``0.12.0`` ``-Python-3.7.2`` ``foss/2019a`` ========== ================= ============== .. _list_software_QJson_491: *QJson* +++++++ QJson is a Qt-based library that maps JSON data to QVariant objects and vice versa. *homepage*: http://qjson.sourceforge.net/ ========= ================================================== version toolchain ========= ================================================== ``0.9.0`` ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b`` ========= ================================================== .. _list_software_QML_234: *QML* +++++ QML is a Python2/3-compatible toolkit for representation learning of properties of molecules and solids. *homepage*: http://www.qmlcode.org ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``0.2.10`` ``-Python-2.7.13`` ``intel/2017a`` ========== ================== =============== .. _list_software_qpth_445: *qpth* ++++++ A fast and differentiable QP solver for PyTorch. *homepage*: https://locuslab.github.io/qpth/ =================== ================= ============== version versionsuffix toolchain =================== ================= ============== ``0.0.13-20190626`` ``-Python-3.7.2`` ``foss/2019a`` =================== ================= ============== .. _list_software_qrupdate_870: *qrupdate* ++++++++++ qrupdate is a Fortran library for fast updates of QR and Cholesky decompositions. *homepage*: https://sourceforge.net/projects/qrupdate/ ========= ======================================================================================================================================== version toolchain ========= ======================================================================================================================================== ``1.1.2`` ``GCC/5.4.0-2.26``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2018a``, ``foss/2018b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ========= ======================================================================================================================================== .. _list_software_QScintilla_1012: *QScintilla* ++++++++++++ QScintilla is a port to Qt of Neil Hodgson's Scintilla C++ editor control *homepage*: https://www.riverbankcomputing.com/software/qscintilla ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``2.9.4`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``2.10`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``2.11.2`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ========== ================== =============================== .. _list_software_Qt_197: *Qt* ++++ Qt is a comprehensive cross-platform C++ application framework. *homepage*: http://qt.io/ ========= ================ ============================================================================================================================================================================================================================================ version versionsuffix toolchain ========= ================ ============================================================================================================================================================================================================================================ ``3.3.8`` ``intel/2016a`` ``4.8.6`` ``system`` ``4.8.7`` ``GCCcore/8.2.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``4.8.7`` ``-GLib-2.48.0`` ``foss/2016a``, ``intel/2016a`` ========= ================ ============================================================================================================================================================================================================================================ .. _list_software_Qt5_250: *Qt5* +++++ Qt is a comprehensive cross-platform C++ application framework. *homepage*: http://qt.io/ ========== ================================================================================= version toolchain ========== ================================================================================= ``5.6.0`` ``foss/2016a``, ``intel/2016a`` ``5.7.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``5.7.1`` ``intel/2016b`` ``5.8.0`` ``foss/2017a``, ``foss/2017b``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``5.9.3`` ``foss/2017b`` ``5.9.8`` ``fosscuda/2018b`` ``5.10.1`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a`` ``5.11.2`` ``foss/2018b`` ``5.12.3`` ``GCCcore/8.2.0`` ``5.13.1`` ``GCCcore/8.3.0`` ========== ================================================================================= .. _list_software_Qt5Webkit_864: *Qt5Webkit* +++++++++++ Qt Port of WebKit. WebKit is an open source web browser engine. *homepage*: https://github.com/qt/qtwebkit ================== ================= version toolchain ================== ================= ``5.212.0-alpha3`` ``GCCcore/8.2.0`` ================== ================= .. _list_software_QtKeychain_1009: *QtKeychain* ++++++++++++ Platform-independent Qt API for storing passwords securely. *homepage*: https://github.com/frankosterfeld/qtkeychain ========= ================================= version toolchain ========= ================================= ``0.9.1`` ``GCCcore/8.2.0``, ``foss/2018b`` ========= ================================= .. _list_software_QTLtools_802: *QTLtools* ++++++++++ QTLtools is a tool set for molecular QTL discovery and analysis. It allows to go from the raw sequence data to collection of molecular Quantitative Trait Loci (QTLs) in few easy-to-perform steps. *homepage*: https://qtltools.github.io/qtltools/ ======= =============== version toolchain ======= =============== ``1.1`` ``intel/2016b`` ======= =============== .. _list_software_qtop_452: *qtop* ++++++ qtop is a nifty command-line tool for monitoring queueing systems, esp. PBS/torque. It tries to fit as much information as possible in your screen's real estate, by stitching together the output of commands like pbsnodes -a, qstat & qstat -q. It is possible to write wrappers for other platforms -people have done so for SGE, OAR etc- or, even examine traces offline and present the sampled information. *homepage*: http://cern.ch/fotis/QTOP/ ======= ============= ========== version versionsuffix toolchain ======= ============= ========== ``53`` ``-1`` ``system`` ======= ============= ========== .. _list_software_Qualimap_826: *Qualimap* ++++++++++ Qualimap 2 is a platform-independent application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data and its derivatives like feature counts. *homepage*: http://qualimap.bioinfo.cipf.es/ ========= ============= ============== version versionsuffix toolchain ========= ============= ============== ``2.2.1`` ``-R-3.6.0`` ``foss/2019a`` ========= ============= ============== .. _list_software_Quandl_613: *Quandl* ++++++++ A Python library for Quandl’s RESTful API. *homepage*: https://pypi.python.org/pypi/Quandl ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``3.4.2`` ``-Python-3.6.4`` ``intel/2018a`` ``3.4.8`` ``foss/2019a`` ========= ================= =============== .. _list_software_QuantumESPRESSO_1375: *QuantumESPRESSO* +++++++++++++++++ Quantum ESPRESSO is an integrated suite of computer codes for electronic-structure calculations and materials modeling at the nanoscale. It is based on density-functional theory, plane waves, and pseudopotentials (both norm-conserving and ultrasoft). *homepage*: https://www.quantum-espresso.org ========= ============= =============================== version versionsuffix toolchain ========= ============= =============================== ``5.3.0`` ``intel/2016.02-GCC-4.9`` ``5.4.0`` ``intel/2016.02-GCC-4.9`` ``5.4.0`` ``-hybrid`` ``foss/2016b`` ``6.0`` ``intel/2016b`` ``6.1`` ``intel/2017a`` ``6.2`` ``intel/2017b`` ``6.2.1`` ``iomkl/2017b`` ``6.3`` ``foss/2018b``, ``intel/2018b`` ``6.4.1`` ``intel/2019a`` ========= ============= =============================== .. _list_software_QUAST_398: *QUAST* +++++++ QUAST evaluates genome assemblies by computing various metrics. It works both with and without reference genomes. The tool accepts multiple assemblies, thus is suitable for comparison. *homepage*: https://github.com/ablab/quast ========= ================== ============================== version versionsuffix toolchain ========= ================== ============================== ``4.6.0`` ``-Python-3.5.2`` ``foss/2016b`` ``4.6.3`` ``-Python-3.6.4`` ``foss/2018a`` ``5.0.2`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a`` ``5.0.2`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================== ============================== .. _list_software_QuaZIP_538: *QuaZIP* ++++++++ QuaZIP is the C++ wrapper for Gilles Vollant's ZIP/UNZIP package (AKA Minizip) using Trolltech's Qt library. *homepage*: https://stachenov.github.io/quazip ========= ================= version toolchain ========= ================= ``0.8.1`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_QuickFF_649: *QuickFF* +++++++++ QuickFF is a Python package developed at the Center for Molecular Modeling (CMM) to quickly derive accurate force fields from ab initio calculations. *homepage*: https://molmod.github.io/QuickFF/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``2.1.4`` ``-Python-2.7.12`` ``intel/2016b`` ``2.2.0`` ``-Python-2.7.14`` ``intel/2017b`` ``2.2.4`` ``-Python-3.7.2`` ``intel/2019a`` ========= ================== =============== .. _list_software_Quip_415: *Quip* ++++++ Quip compresses next-generation sequencing data with extreme prejudice. It supports input and output in the FASTQ and SAM/BAM formats, compressing large datasets to as little as 15% of their original size. *homepage*: http://homes.cs.washington.edu/~dcjones/quip ========= ============= version toolchain ========= ============= ``1.1.8`` ``GCC/4.8.2`` ========= ============= .. _list_software_Quorum_649: *Quorum* ++++++++ QuorUM is an error corrector for Illumina reads *homepage*: http://www.genome.umd.edu/quorum.html ========= =============== version toolchain ========= =============== ``1.1.1`` ``intel/2017a`` ========= =============== .. _list_software_QuTiP_467: *QuTiP* +++++++ QuTiP is open-source software for simulating the dynamics of open quantum systems. *homepage*: http://qutip.org ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``4.1.0`` ``-Python-2.7.12`` ``intel/2016b`` ``4.3.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ========= ================== =============================== .. _list_software_Qwt_316: *Qwt* +++++ The Qwt library contains GUI Components and utility classes which are primarily useful for programs with a technical background. *homepage*: http://qwt.sourceforge.net/ ========= ==================================================== version toolchain ========= ==================================================== ``6.1.2`` ``intel/2016a`` ``6.1.3`` ``foss/2016b``, ``intel/2016b`` ``6.1.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018b`` ========= ==================================================== .. _list_software_QwtPolar_826: *QwtPolar* ++++++++++ The QwtPolar library contains classes for displaying values on a polar coordinate system. *homepage*: http://qwtpolar.sourceforge.net/ ========= ================================================== version toolchain ========= ================================================== ``1.1.1`` ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2016b`` ========= ================================================== .. _list_software_letter_r: *R* --- :ref:`list_software_R_82` - :ref:`list_software_R-bundle-Bioconductor_2065` - :ref:`list_software_R-keras_661` - :ref:`list_software_R-tesseract_1101` - :ref:`list_software_Racon_499` - :ref:`list_software_Ragout_626` - :ref:`list_software_randfold_842` - :ref:`list_software_randrproto_1099` - :ref:`list_software_RapidJSON_810` - :ref:`list_software_rapidtide_950` - :ref:`list_software_Rascaf_592` - :ref:`list_software_RASPA2_425` - :ref:`list_software_RAxML_420` - :ref:`list_software_RBFOpt_525` - :ref:`list_software_Rcorrector_1061` - :ref:`list_software_rCUDA_399` - :ref:`list_software_RDFlib_531` - :ref:`list_software_RDKit_446` - :ref:`list_software_RDP-Classifier_1304` - :ref:`list_software_re2c_364` - :ref:`list_software_Reads2snp_882` - :ref:`list_software_Redundans_932` - :ref:`list_software_ReFrame_674` - :ref:`list_software_RELION_457` - :ref:`list_software_REMORA_454` - :ref:`list_software_renderproto_1204` - :ref:`list_software_RepastHPC_842` - :ref:`list_software_RepeatMasker_1220` - :ref:`list_software_requests_892` - :ref:`list_software_RERconverge_1090` - :ref:`list_software_rgdal_522` - :ref:`list_software_rgeos_544` - :ref:`list_software_rhdf5_473` - :ref:`list_software_rioxarray_993` - :ref:`list_software_rjags_535` - :ref:`list_software_Rmath_508` - :ref:`list_software_RMBlast_661` - :ref:`list_software_RNA-SeQC_602` - :ref:`list_software_RNAclust_780` - :ref:`list_software_RNAcode_636` - :ref:`list_software_RNAIndel_717` - :ref:`list_software_rnaQUAST_719` - :ref:`list_software_RNAz_347` - :ref:`list_software_Roary_525` - :ref:`list_software_ROI_PAC_541` - :ref:`list_software_ROME_307` - :ref:`list_software_ROOT_324` - :ref:`list_software_rootpy_685` - :ref:`list_software_Rosetta_738` - :ref:`list_software_rpmrebuild_1078` - :ref:`list_software_rpy2_397` - :ref:`list_software_RQGIS3_441` - :ref:`list_software_RSEM_311` - :ref:`list_software_RSeQC_414` - :ref:`list_software_RStan_488` - :ref:`list_software_RTG-Tools_811` - :ref:`list_software_Rtree_514` - :ref:`list_software_Ruby_418` - :ref:`list_software_Rust_430` .. _list_software_R_82: *R* +++ R is a free software environment for statistical computing and graphics. *homepage*: https://www.r-project.org/ ========= ================== =================================================== version versionsuffix toolchain ========= ================== =================================================== ``3.2.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a`` ``3.2.3`` ``-bare`` ``foss/2016a``, ``intel/2016a`` ``3.2.3`` ``-libX11-1.6.3`` ``intel/2016a`` ``3.3.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``3.3.3`` ``-X11-20160819`` ``foss/2016b``, ``intel/2016b`` ``3.3.3`` ``-X11-20170314`` ``intel/2017a`` ``3.4.0`` ``-X11-20170314`` ``intel/2017a`` ``3.4.1`` ``-X11-20160819`` ``foss/2016b`` ``3.4.3`` ``-X11-20171023`` ``foss/2017b``, ``intel/2017b`` ``3.4.4`` ``-X11-20180131`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` ``3.5.0`` ``-X11-20180131`` ``iomkl/2018a`` ``3.5.1`` ``foss/2018b``, ``intel/2018b`` ``3.5.1`` ``-Python-2.7.15`` ``foss/2018b`` ``3.6.0`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``3.6.2`` ``foss/2019b``, ``fosscuda/2019b`` ========= ================== =================================================== .. _list_software_R-bundle-Bioconductor_2065: *R-bundle-Bioconductor* +++++++++++++++++++++++ Bioconductor provides tools for the analysis and coprehension of high-throughput genomic data. *homepage*: https://bioconductor.org ======= ============= =============================== version versionsuffix toolchain ======= ============= =============================== ``3.2`` ``-R-3.2.3`` ``foss/2016a``, ``intel/2016a`` ``3.3`` ``-R-3.3.1`` ``intel/2016b`` ``3.5`` ``-R-3.4.0`` ``intel/2017a`` ``3.6`` ``-R-3.4.3`` ``foss/2017b``, ``intel/2017b`` ``3.6`` ``-R-3.4.4`` ``intel/2018a`` ``3.7`` ``-R-3.5.0`` ``iomkl/2018a`` ``3.7`` ``-R-3.5.1`` ``foss/2018b`` ``3.8`` ``-R-3.5.1`` ``foss/2018b`` ``3.9`` ``-R-3.6.0`` ``foss/2019a`` ======= ============= =============================== .. _list_software_R-keras_661: *R-keras* +++++++++ Interface to 'Keras' , a high-level neural networks 'API'. *homepage*: https://cran.r-project.org/web/packages/keras =========== ========================= ================================== version versionsuffix toolchain =========== ========================= ================================== ``2.1.6`` ``-R-3.4.4`` ``foss/2018a`` ``2.2.5.0`` ``-Python-3.7.2-R-3.6.0`` ``foss/2019a``, ``fosscuda/2019a`` =========== ========================= ================================== .. _list_software_R-tesseract_1101: *R-tesseract* +++++++++++++ The R extension for using tesseract *homepage*: https://cran.r-project.org/package=tesseract ======= ============= ============== version versionsuffix toolchain ======= ============= ============== ``4.0`` ``-R-3.5.1`` ``foss/2018b`` ======= ============= ============== .. _list_software_Racon_499: *Racon* +++++++ Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads. *homepage*: https://github.com/lbcb-sci/racon ========= ================= version toolchain ========= ================= ``1.3.2`` ``GCCcore/8.2.0`` ``1.4.7`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_Ragout_626: *Ragout* ++++++++ Ragout (Reference-Assisted Genome Ordering UTility) is a tool for chromosome assembly using multiple references. Given a set of assembly fragments (contigs/scaffolds) and one or multiple related references (complete or draft), it produces a chromosome-scale assembly (as a set of scaffolds). *homepage*: http://fenderglass.github.io/Ragout/ ======= ================== ============== version versionsuffix toolchain ======= ================== ============== ``2.0`` ``-Python-2.7.12`` ``foss/2016b`` ======= ================== ============== .. _list_software_randfold_842: *randfold* ++++++++++ Minimum free energy of folding randomization test software *homepage*: http://bioinformatics.psb.ugent.be/software/details/Randfold ========= =============================== version toolchain ========= =============================== ``2.0.1`` ``foss/2018b``, ``intel/2016b`` ========= =============================== .. _list_software_randrproto_1099: *randrproto* ++++++++++++ Xrandr protocol and ancillary headers *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== version toolchain ========= =============================== ``1.5.0`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_RapidJSON_810: *RapidJSON* +++++++++++ A fast JSON parser/generator for C++ with both SAX/DOM style API *homepage*: https://rapidjson.org ========= ================= version toolchain ========= ================= ``1.1.0`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_rapidtide_950: *rapidtide* +++++++++++ Rapidtide is a suite of python programs used to perform time delay analysis on functional imaging data to find time lagged correlations between the voxelwise time series and other time series. *homepage*: https://rapidtide.readthedocs.io ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``1.8.0`` ``-Python-3.7.2`` ``intel/2019a`` ========= ================= =============== .. _list_software_Rascaf_592: *Rascaf* ++++++++ Rascaf (RnA-seq SCAFfolder) uses continuity and order information from paired-end RNA-seq reads to improve a draft assembly, particularly in the gene regions. *homepage*: https://github.com/mourisl/Rascaf ========= =============== version toolchain ========= =============== ``1.0.2`` ``intel/2017a`` ========= =============== .. _list_software_RASPA2_425: *RASPA2* ++++++++ A general purpose classical simulation package that can be used for the simulation of molecules in gases, fluids, zeolites, aluminosilicates, metal-organic frameworks, carbon nanotubes and external fields. *homepage*: https://github.com/numat/RASPA2 ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``2.0.3`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== .. _list_software_RAxML_420: *RAxML* +++++++ RAxML search algorithm for maximum likelihood based inference of phylogenetic trees. *homepage*: https://github.com/stamatak/standard-RAxML ========== ================ ================================================ version versionsuffix toolchain ========== ================ ================================================ ``8.2.4`` ``-hybrid-avx2`` ``foss/2016a`` ``8.2.9`` ``-hybrid-avx2`` ``foss/2016a`` ``8.2.10`` ``-hybrid-avx2`` ``intel/2017a`` ``8.2.11`` ``-hybrid-avx`` ``foss/2017b``, ``intel/2017b`` ``8.2.11`` ``-hybrid-avx2`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``8.2.11`` ``-hybrid-sse3`` ``foss/2017b``, ``intel/2017b`` ``8.2.12`` ``-hybrid-avx2`` ``intel/2019a`` ========== ================ ================================================ .. _list_software_RBFOpt_525: *RBFOpt* ++++++++ RBFOpt is a Python library for black-box optimization (also known as derivative-free optimization). *homepage*: https://github.com/coin-or/rbfopt ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``4.1.1`` ``intel/2019a`` ``4.1.1`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================= =============== .. _list_software_Rcorrector_1061: *Rcorrector* ++++++++++++ Rcorrector(RNA-seq error CORRECTOR) is a kmer-based error correction method for RNA-seq data. *homepage*: https://github.com/mourisl/Rcorrector ========= =============== version toolchain ========= =============== ``1.0.2`` ``intel/2017a`` ========= =============== .. _list_software_rCUDA_399: *rCUDA* +++++++ The rCUDA Framework enables the concurrent usage of CUDA-compatible devices remotely. *homepage*: http://www.rcuda.net/ ========= ============================== ========== version versionsuffix toolchain ========= ============================== ========== ``4.0.1`` ``_linux_64_Ubuntu10.04`` ``system`` ``5.0`` ``_linux_64_scientificLinux6`` ``system`` ========= ============================== ========== .. _list_software_RDFlib_531: *RDFlib* ++++++++ RDFLib is a Python library for working with RDF, a simple yet powerful language for representing information. *homepage*: https://github.com/RDFLib/rdflib ========= ============== version toolchain ========= ============== ``4.2.2`` ``foss/2019a`` ========= ============== .. _list_software_RDKit_446: *RDKit* +++++++ RDKit is a collection of cheminformatics and machine-learning software written in C++ and Python. *homepage*: https://www.rdkit.org ============= ================= =============== version versionsuffix toolchain ============= ================= =============== ``2018.09.3`` ``-Python-3.6.6`` ``intel/2018b`` ============= ================= =============== .. _list_software_RDP-Classifier_1304: *RDP-Classifier* ++++++++++++++++ The RDP Classifier is a naive Bayesian classifier that can rapidly and accurately provides taxonomic assignments from domain to genus, with confidence estimates for each assignment. *homepage*: http://sourceforge.net/projects/rdp-classifier ======== ================== ========== version versionsuffix toolchain ======== ================== ========== ``2.7`` ``-Java-1.7.0_60`` ``system`` ``2.12`` ``-Java-1.8`` ``system`` ======== ================== ========== .. _list_software_re2c_364: *re2c* ++++++ re2c is a free and open-source lexer generator for C and C++. Its main goal is generating fast lexers: at least as fast as their reasonably optimized hand-coded counterparts. Instead of using traditional table-driven approach, re2c encodes the generated finite state automata directly in the form of conditional jumps and comparisons. *homepage*: https://re2c.org/ ========= ================= version toolchain ========= ================= ``1.1.1`` ``GCCcore/8.2.0`` ``1.2.1`` ``GCCcore/8.3.0`` ========= ================= .. _list_software_Reads2snp_882: *Reads2snp* +++++++++++ reads2snp is a SNP and genotype caller: it predicts the genotype of distinct individuals at distinct positions of a set of sequences based on read mapping / read counts. Its typical input is a bam file. Its typical output is a vcf file. It is written in C++, based on the bio++ libraries, multi-threaded with openMP, available under Linux and MacOS *homepage*: http://kimura.univ-montp2.fr/PopPhyl/index.php?section=tools ======= ========== version toolchain ======= ========== ``2.0`` ``system`` ======= ========== .. _list_software_Redundans_932: *Redundans* +++++++++++ Redundans is a pipeline that assists an assembly of heterozygous/polymorphic genomes. *homepage*: https://github.com/lpryszcz/redundans ========= =============== version toolchain ========= =============== ``0.13c`` ``intel/2017b`` ========= =============== .. _list_software_ReFrame_674: *ReFrame* +++++++++ ReFrame is a framework for writing regression tests for HPC systems. *homepage*: https://github.com/eth-cscs/reframe ======== ========== version toolchain ======== ========== ``2.18`` ``system`` ``2.19`` ``system`` ``2.20`` ``system`` ======== ========== .. _list_software_RELION_457: *RELION* ++++++++ RELION (for REgularised LIkelihood OptimisatioN, pronounce rely-on) is a stand-alone computer program that employs an empirical Bayesian approach to refinement of (multiple) 3D reconstructions or 2D class averages in electron cryo-microscopy (cryo-EM). *homepage*: http://www2.mrc-lmb.cam.ac.uk/relion/index.php/Main_Page ======================= ================ ============================================================================================================ version versionsuffix toolchain ======================= ================ ============================================================================================================ ``1.4`` ``intel/2016b`` ``1.4`` ``-single`` ``intel/2016b`` ``2.0.1`` ``intel/2016b`` ``2.1`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``fosscuda/2018a``, ``intel/2017b``, ``intelcuda/2017b`` ``2.1`` ``-CUDA-9.1.85`` ``foss/2018a`` ``3.0.4`` ``foss/2017b``, ``intel/2017b`` ``3.0_beta.2018.08.02`` ``fosscuda/2018a``, ``intel/2018a`` ======================= ================ ============================================================================================================ .. _list_software_REMORA_454: *REMORA* ++++++++ REsource MOnitoring for Remote Applications *homepage*: https://github.com/TACC/remora ========= ================================================================ version toolchain ========= ================================================================ ``1.8.2`` ``foss/2017a``, ``foss/2018a``, ``intel/2017a``, ``intel/2018a`` ``1.8.3`` ``gompi/2019a`` ========= ================================================================ .. _list_software_renderproto_1204: *renderproto* +++++++++++++ Xrender protocol and ancillary headers *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ======== ================================================================== version toolchain ======== ================================================================== ``0.11`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017b`` ======== ================================================================== .. _list_software_RepastHPC_842: *RepastHPC* +++++++++++ The Repast Suite is a family of advanced, free, and open source agent-based modeling and simulation platforms that have collectively been under continuous development for over 15 years: Repast for High Performance Computing 2.2.0, released on 30 September 2016, is a lean and expert-focused C++-based modeling system that is designed for use on large computing clusters and supercomputers. *homepage*: https://repast.github.io/ ========= ============== version toolchain ========= ============== ``2.2.0`` ``foss/2016a`` ========= ============== .. _list_software_RepeatMasker_1220: *RepeatMasker* ++++++++++++++ RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. *homepage*: http://www.repeatmasker.org/ ============ ====================== ========================================================== version versionsuffix toolchain ============ ====================== ========================================================== ``4.0.8`` ``-Perl-5.26.0-HMMER`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ``4.0.8`` ``-Perl-5.28.0-HMMER`` ``intel/2018b`` ``4.0.9-p2`` ``-HMMER`` ``gompi/2019b`` ============ ====================== ========================================================== .. _list_software_requests_892: *requests* ++++++++++ Python http for humans *homepage*: https://pypi.python.org/pypi/requests ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``2.10.0`` ``-Python-2.7.11`` ``foss/2016a`` ``2.10.0`` ``-Python-3.5.1`` ``foss/2016a`` ``2.11.1`` ``-Python-2.7.12`` ``intel/2016b`` ``2.11.1`` ``-Python-3.5.2`` ``intel/2016b`` ``2.13.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ========== ================== =============================== .. _list_software_RERconverge_1090: *RERconverge* +++++++++++++ RERconverge is a set of software written in R that estimates the correlation between relative evolutionary rates of genes and the evolution of a convergent binary or continuous trait across a phylogeny. *homepage*: https://github.com/nclark-lab/RERconverge ========= ============= =============================== version versionsuffix toolchain ========= ============= =============================== ``0.1.0`` ``-R-3.4.3`` ``foss/2017b``, ``intel/2017b`` ========= ============= =============================== .. _list_software_rgdal_522: *rgdal* +++++++ Provides bindings to the 'Geospatial' Data Abstraction Library ('GDAL') (>= 1.11.4 and <= 2.5.0) and access to projection/transformation operations from the 'PROJ.4' library. *homepage*: http://rgdal.r-forge.r-project.org/ ========= ============= ============== version versionsuffix toolchain ========= ============= ============== ``1.4-4`` ``-R-3.6.0`` ``foss/2019a`` ========= ============= ============== .. _list_software_rgeos_544: *rgeos* +++++++ R interface to Geometry Engine - Open Source (GEOS) using the C API for topology operations on geometries *homepage*: https://cran.r-project.org/web/packages/rgeos/ ========== ============= =============== version versionsuffix toolchain ========== ============= =============== ``0.3-17`` ``-R-3.2.3`` ``intel/2016a`` ``0.5-1`` ``-R-3.6.0`` ``foss/2019a`` ========== ============= =============== .. _list_software_rhdf5_473: *rhdf5* +++++++ This R/Bioconductor package provides an interface between HDF5 and R. *homepage*: https://bioconductor.org/packages/release/bioc/html/rhdf5.html ========== ============= =============== version versionsuffix toolchain ========== ============= =============== ``2.16.0`` ``-R-3.2.3`` ``intel/2016a`` ``2.18.0`` ``-R-3.3.1`` ``intel/2016b`` ========== ============= =============== .. _list_software_rioxarray_993: *rioxarray* +++++++++++ geospatial xarray extension powered by rasterio *homepage*: https://github.com/corteva/rioxarray ========== ================= =============== version versionsuffix toolchain ========== ================= =============== ``0.0.12`` ``-Python-3.7.2`` ``intel/2019a`` ========== ================= =============== .. _list_software_rjags_535: *rjags* +++++++ The rjags package is an interface to the JAGS library. *homepage*: http://cran.r-project.org/web/packages/rjags ======= ============= =============== version versionsuffix toolchain ======= ============= =============== ``4-6`` ``-R-3.4.0`` ``intel/2017a`` ``4-6`` ``-R-3.4.3`` ``intel/2017b`` ``4-8`` ``-R-3.5.1`` ``foss/2018b`` ======= ============= =============== .. _list_software_Rmath_508: *Rmath* +++++++ Rmath is the standalone version of the R math library. Rmath can be used in your own C/C++ routines. *homepage*: https://www.r-project.org/ ========= =============== version toolchain ========= =============== ``3.3.1`` ``intel/2016b`` ========= =============== .. _list_software_RMBlast_661: *RMBlast* +++++++++ RMBlast is a RepeatMasker compatible version of the standard NCBI BLAST suite. The primary difference between this distribution and the NCBI distribution is the addition of a new program 'rmblastn' for use with RepeatMasker and RepeatModeler. *homepage*: http://www.repeatmasker.org/RMBlast.html ========== ================== ============== version versionsuffix toolchain ========== ================== ============== ``2.2.28`` ``-Python-2.7.11`` ``foss/2016a`` ========== ================== ============== .. _list_software_RNA-SeQC_602: *RNA-SeQC* ++++++++++ RNA-SeQC is a java program which computes a series of quality control metrics for RNA-seq data. The input can be one or more BAM files. The output consists of HTML reports and tab delimited files of metrics data. This program can be valuable for comparing sequencing quality across different samples or experiments to evaluate different experimental parameters. It can also be run on individual samples as a means of quality control before continuing with downstream analysis. *homepage*: https://software.broadinstitute.org/cancer/cga/rna-seqc ========= =================== ============== version versionsuffix toolchain ========= =================== ============== ``1.1.8`` ``-Java-1.8`` ``foss/2018b`` ``1.1.8`` ``-Java-1.8.0_121`` ``foss/2016b`` ========= =================== ============== .. _list_software_RNAclust_780: *RNAclust* ++++++++++ RNAclust is a perl script summarizing all the single steps required for clustering of structured RNA motifs, i.e. identifying groups of RNA sequences sharing a secondary structure motif. It requires as input a multiple FASTA file. *homepage*: http://www.bioinf.uni-leipzig.de/~kristin/Software/RNAclust/ ======= ================= ============== version versionsuffix toolchain ======= ================= ============== ``1.3`` ``-Perl-5.24.0`` ``foss/2016b`` ``1.3`` ``-Python-3.6.6`` ``foss/2018b`` ======= ================= ============== .. _list_software_RNAcode_636: *RNAcode* +++++++++ RNAcode - Analyze the protein coding potential in multiple sequence alignments *homepage*: https://wash.github.io/rnacode/ ======= ============== version toolchain ======= ============== ``0.3`` ``foss/2017a`` ======= ============== .. _list_software_RNAIndel_717: *RNAIndel* ++++++++++ RNAIndel calls coding indels and classifies them into somatic, germline, and artifact from tumor RNA-Seq data. *homepage*: https://github.com/stjude/RNAIndel ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``0.3.0`` ``-Python-3.6.6`` ``intel/2018b`` ``1.0.0`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================= =============== .. _list_software_rnaQUAST_719: *rnaQUAST* ++++++++++ rnaQUAST is a tool for evaluating RNA-Seq assemblies using reference genome and gene database. In addition, rnaQUAST is also capable of estimating gene database coverage by raw reads and de novo quality assessment using third-party software. *homepage*: http://cab.spbu.ru/software/rnaquast/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.5.2`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== ============== .. _list_software_RNAz_347: *RNAz* ++++++ RNAz is a program for predicting structurally conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments. *homepage*: http://www.tbi.univie.ac.at/~wash/RNAz/ ======= ============================== version toolchain ======= ============================== ``2.1`` ``foss/2016b``, ``foss/2018b`` ======= ============================== .. _list_software_Roary_525: *Roary* +++++++ Rapid large-scale prokaryote pan genome analysis *homepage*: https://github.com/sanger-pathogens/Roary ========== ================ =============== version versionsuffix toolchain ========== ================ =============== ``3.12.0`` ``system`` ``3.12.0`` ``-Perl-5.26.1`` ``intel/2018a`` ========== ================ =============== .. _list_software_ROI_PAC_541: *ROI_PAC* +++++++++ Repeat Orbit Interferometry PACkage (ROI_PAC), software for processing synthetic aperture radar data to produce differential interferograms *homepage*: http://roipac.org/ ========= ================ =============== version versionsuffix toolchain ========= ================ =============== ``3.0.1`` ``-Perl-5.24.1`` ``intel/2017a`` ========= ================ =============== .. _list_software_ROME_307: *ROME* ++++++ The ROME (Refinement and Optimization via Machine Learning for cryo-EM) Software package is one of the major research products at the Intel® PCCSB. *homepage*: https://ipccsb.dfci.harvard.edu/rome ========= ================= version toolchain ========= ================= ``1.1.2`` ``intel/2019.02`` ========= ================= .. _list_software_ROOT_324: *ROOT* ++++++ The ROOT system provides a set of OO frameworks with all the functionality needed to handle and analyze large amounts of data in a very efficient way. *homepage*: http://root.cern.ch/drupal/ ============ ================== =============================== version versionsuffix toolchain ============ ================== =============================== ``6.10.02`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``6.10.04`` ``-Python-2.7.13`` ``intel/2017a`` ``6.10.08`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``6.14.06`` ``-Python-2.7.15`` ``foss/2018b`` ``v5.34.34`` ``-Python-2.7.11`` ``intel/2016a`` ``v5.34.36`` ``-Python-2.7.11`` ``intel/2016a`` ``v6.06.02`` ``-Python-2.7.12`` ``intel/2016b`` ``v6.08.02`` ``-Python-2.7.11`` ``foss/2016a`` ============ ================== =============================== .. _list_software_rootpy_685: *rootpy* ++++++++ The rootpy project is a community-driven initiative aiming to provide a more pythonic interface with ROOT on top of the existing PyROOT bindings. Given Python’s reflective and dynamic nature, rootpy also aims to improve ROOT design flaws and supplement existing ROOT functionality. The scientific Python community also offers a multitude of powerful packages such as SciPy, NumPy, matplotlib, scikit-learn, and PyTables, but a suitable interface between them and ROOT has been lacking. rootpy provides the interfaces and conversion mechanisms required to liberate your data and to take advantage of these alternatives if needed. *homepage*: http://www.rootpy.org/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``0.8.0`` ``-Python-2.7.11`` ``foss/2016a`` ========= ================== ============== .. _list_software_Rosetta_738: *Rosetta* +++++++++ Rosetta is the premier software suite for modeling macromolecular structures. As a flexible, multi-purpose application, it includes tools for structure prediction, design, and remodeling of proteins and nucleic acids. *homepage*: https://www.rosettacommons.org ================= ============== version toolchain ================= ============== ``3.7`` ``foss/2016b`` ``2016.13.58602`` ``foss/2016a`` ``2016.46.59086`` ``foss/2016b`` ================= ============== .. _list_software_rpmrebuild_1078: *rpmrebuild* ++++++++++++ rpmrebuild is a tool to build an RPM file from a package that has already been installed in a basic use *homepage*: http://rpmrebuild.sourceforge.net/ ======== ========== version toolchain ======== ========== ``2.11`` ``system`` ======== ========== .. _list_software_rpy2_397: *rpy2* ++++++ rpy2 is a redesign and rewrite of rpy. It is providing a low-level interface to R from Python, a proposed high-level interface, including wrappers to graphical libraries, as well as R-like structures and functions. *homepage*: http://rpy.sourceforge.net/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``2.7.9`` ``-Python-2.7.12`` ``foss/2016b`` ``2.8.2`` ``-Python-2.7.13`` ``intel/2017a`` ========= ================== =============== .. _list_software_RQGIS3_441: *RQGIS3* ++++++++ RQGIS3 establishes an interface between R and QGIS3, i.e., it allows the user to access QGIS3 functionalities from within R. *homepage*: https://github.com/r-spatial/RQGIS3 ============ ============= ============== version versionsuffix toolchain ============ ============= ============== ``20190903`` ``-R-3.6.0`` ``foss/2019a`` ============ ============= ============== .. _list_software_RSEM_311: *RSEM* ++++++ RNA-Seq by Expectation-Maximization *homepage*: http://deweylab.github.io/RSEM/ ========== ================================================ version toolchain ========== ================================================ ``1.2.26`` ``GNU/4.9.3-2.25`` ``1.2.30`` ``foss/2016a``, ``intel/2016b`` ``1.3.0`` ``foss/2016b``, ``intel/2017a`` ``1.3.1`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``1.3.2`` ``foss/2018b`` ========== ================================================ .. _list_software_RSeQC_414: *RSeQC* +++++++ RSeQC provides a number of useful modules that can comprehensively evaluate high throughput sequence data especially RNA-seq data. Some basic modules quickly inspect sequence quality, nucleotide composition bias, PCR bias and GC bias, while RNA-seq specific modules evaluate sequencing saturation, mapped reads distribution, coverage uniformity, strand specificity, transcript level RNA integrity etc. *homepage*: http://rseqc.sourceforge.net/ ========= ========================== =============== version versionsuffix toolchain ========= ========================== =============== ``2.6.4`` ``-Python-2.7.12-R-3.3.1`` ``foss/2016b`` ``2.6.4`` ``-Python-2.7.14`` ``intel/2018a`` ``3.0.0`` ``-Python-3.6.6`` ``foss/2018b`` ========= ========================== =============== .. _list_software_RStan_488: *RStan* +++++++ RStan is the R interface to Stan. Stan is a state-of-the-art platform for statistical modeling and high-performance statistical computation. *homepage*: https://github.com/stan-dev/rstan ========== ============= =============================== version versionsuffix toolchain ========== ============= =============================== ``2.18.2`` ``-R-3.4.3`` ``foss/2017b``, ``intel/2017b`` ``2.18.2`` ``-R-3.5.1`` ``foss/2018b`` ========== ============= =============================== .. _list_software_RTG-Tools_811: *RTG-Tools* +++++++++++ RTG Tools contains utilities to easily manipulate and accurately compare multiple VCF files, as well as utilities for processing other common NGS data formats. *homepage*: https://www.realtimegenomics.com/products/rtg-tools ========= ============= ========== version versionsuffix toolchain ========= ============= ========== ``3.9.1`` ``-Java-1.8`` ``system`` ========= ============= ========== .. _list_software_Rtree_514: *Rtree* +++++++ Rtree is a ctypes Python wrapper of libspatialindex that provides a number of advanced spatial indexing features for the spatially curious Python user. *homepage*: http://toblerity.org/rtree/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.8.3`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============== .. _list_software_Ruby_418: *Ruby* ++++++ Ruby is a dynamic, open source programming language with a focus on simplicity and productivity. It has an elegant syntax that is natural to read and easy to write. *homepage*: https://www.ruby-lang.org ========= ================================================ version toolchain ========= ================================================ ``2.1.6`` ``system`` ``2.3.1`` ``intel/2016b``, ``system`` ``2.3.3`` ``system`` ``2.3.4`` ``system`` ``2.4.2`` ``foss/2017b`` ``2.5.0`` ``foss/2018a``, ``intel/2017a``, ``intel/2017b`` ``2.5.1`` ``intel/2018a`` ``2.6.1`` ``GCCcore/7.3.0`` ``2.6.3`` ``GCCcore/8.2.0`` ========= ================================================ .. _list_software_Rust_430: *Rust* ++++++ Rust is a systems programming language that runs blazingly fast, prevents segfaults, and guarantees thread safety. *homepage*: https://www.rust-lang.org ========== ================= version toolchain ========== ================= ``1.8.0`` ``foss/2016a`` ``1.12.0`` ``foss/2016b`` ``1.12.1`` ``foss/2016b`` ``1.18.0`` ``foss/2017a`` ``1.21.0`` ``foss/2017b`` ``1.22.1`` ``GCCcore/6.4.0`` ``1.29.2`` ``GCCcore/7.3.0`` ``1.30.1`` ``GCCcore/6.4.0`` ``1.35.0`` ``GCCcore/8.2.0`` ``1.37.0`` ``GCCcore/8.3.0`` ========== ================= .. _list_software_letter_s: *S* --- :ref:`list_software_S-Lang_514` - :ref:`list_software_S4_135` - :ref:`list_software_SAGE_288` - :ref:`list_software_Sailfish_819` - :ref:`list_software_SALib_427` - :ref:`list_software_Salmon_618` - :ref:`list_software_SALMON-TDDFT_877` - :ref:`list_software_Sambamba_788` - :ref:`list_software_Samcef_591` - :ref:`list_software_samclip_745` - :ref:`list_software_SAMtools_786` - :ref:`list_software_SAS_231` - :ref:`list_software_savvy_569` - :ref:`list_software_Saxon-HE_707` - :ref:`list_software_sbt_329` - :ref:`list_software_ScaLAPACK_707` - :ref:`list_software_Scalasca_795` - :ref:`list_software_SCALCE_427` - :ref:`list_software_sciClone_816` - :ref:`list_software_ScientificPython_1667` - :ref:`list_software_scikit-allel_1214` - :ref:`list_software_scikit-image_1207` - :ref:`list_software_scikit-learn_1222` - :ref:`list_software_scikit-multilearn_1777` - :ref:`list_software_scikit-optimize_1573` - :ref:`list_software_SCIPhI_480` - :ref:`list_software_scipy_552` - :ref:`list_software_SciPy-bundle_1167` - :ref:`list_software_SCnorm_594` - :ref:`list_software_Scoary_625` - :ref:`list_software_SCons_486` - :ref:`list_software_SCOOP_388` - :ref:`list_software_Score-P_633` - :ref:`list_software_SCOTCH_452` - :ref:`list_software_scp_326` - :ref:`list_software_Scrappie_823` - :ref:`list_software_SDCC_285` - :ref:`list_software_SDL2_277` - :ref:`list_software_Seaborn_714` - :ref:`list_software_SearchGUI_827` - :ref:`list_software_segemehl_842` - :ref:`list_software_SelEstim_806` - :ref:`list_software_sep_328` - :ref:`list_software_Seq-Gen_624` - :ref:`list_software_seq2HLA_592` - :ref:`list_software_SeqAn_472` - :ref:`list_software_SeqAn3_523` - :ref:`list_software_Seqmagick_917` - :ref:`list_software_SeqPrep_704` - :ref:`list_software_seqtk_552` - :ref:`list_software_Serf_400` - :ref:`list_software_setuptools_1122` - :ref:`list_software_Seurat_628` - :ref:`list_software_Shannon_725` - :ref:`list_software_shapAAR_640` - :ref:`list_software_SHAPEIT_526` - :ref:`list_software_sharutils_991` - :ref:`list_software_shift_542` - :ref:`list_software_SHORE_385` - :ref:`list_software_Short-Pair_969` - :ref:`list_software_shovill_769` - :ref:`list_software_shrinkwrap_1097` - :ref:`list_software_Sibelia_697` - :ref:`list_software_sickle_635` - :ref:`list_software_Siesta_617` - :ref:`list_software_SimPEG_517` - :ref:`list_software_SIMPLE_458` - :ref:`list_software_SimpleElastix_1348` - :ref:`list_software_SimpleITK_850` - :ref:`list_software_simpy_562` - :ref:`list_software_SimVascular_1130` - :ref:`list_software_SingleM_687` - :ref:`list_software_Singularity_1179` - :ref:`list_software_SIONlib_624` - :ref:`list_software_SIP_236` - :ref:`list_software_SKESA_375` - :ref:`list_software_sketchmap_960` - :ref:`list_software_skewer_657` - :ref:`list_software_SLEPc_407` - :ref:`list_software_slepc4py_820` - :ref:`list_software_sleuth_661` - :ref:`list_software_slidingwindow_1410` - :ref:`list_software_smafa_520` - :ref:`list_software_smallgenomeutilities_2160` - :ref:`list_software_SMARTdenovo_1042` - :ref:`list_software_Smoldyn_742` - :ref:`list_software_SMRT-Link_769` - :ref:`list_software_snakemake_944` - :ref:`list_software_SNAP_306` - :ref:`list_software_SNAPE-pooled_1063` - :ref:`list_software_snaphu_655` - :ref:`list_software_snappy_667` - :ref:`list_software_snippy_675` - :ref:`list_software_snpEff_610` - :ref:`list_software_SNPhylo_685` - :ref:`list_software_SOAPaligner_1045` - :ref:`list_software_SOAPdenovo-Trans_1523` - :ref:`list_software_SOAPdenovo2_1008` - :ref:`list_software_SOAPfuse_742` - :ref:`list_software_socat_538` - :ref:`list_software_SolexaQA++_852` - :ref:`list_software_SortMeRNA_827` - :ref:`list_software_Spack_498` - :ref:`list_software_SPAdes_544` - :ref:`list_software_spaln_542` - :ref:`list_software_Spark_513` - :ref:`list_software_sparsehash_1074` - :ref:`list_software_spectral.methods_1664` - :ref:`list_software_spglib_641` - :ref:`list_software_spglib-python_1360` - :ref:`list_software_Sphinx_634` - :ref:`list_software_SpiceyPy_822` - :ref:`list_software_SpiecEasi_886` - :ref:`list_software_SPLASH_459` - :ref:`list_software_SpliceMap_894` - :ref:`list_software_splitRef_841` - :ref:`list_software_SPRNG_394` - :ref:`list_software_Spyder_631` - :ref:`list_software_SQLite_562` - :ref:`list_software_SqueezeMeta_1129` - :ref:`list_software_SRA-Toolkit_1017` - :ref:`list_software_SRPRISM_560` - :ref:`list_software_SSAHA2_418` - :ref:`list_software_SSPACE_Basic_1024` - :ref:`list_software_Stacks_617` - :ref:`list_software_STAMP_389` - :ref:`list_software_StaMPS_536` - :ref:`list_software_Stampy_638` - :ref:`list_software_STAR_314` - :ref:`list_software_STAR-Fusion_987` - :ref:`list_software_Stata_509` - :ref:`list_software_statsmodels_1203` - :ref:`list_software_STIR_322` - :ref:`list_software_STREAM_460` - :ref:`list_software_strelka_758` - :ref:`list_software_StringTie_921` - :ref:`list_software_Structure_977` - :ref:`list_software_Subread_710` - :ref:`list_software_Subversion_1072` - :ref:`list_software_suds_447` - :ref:`list_software_SuiteSparse_1144` - :ref:`list_software_SUMACLUST_705` - :ref:`list_software_SUMATRA_541` - :ref:`list_software_SUNDIALS_611` - :ref:`list_software_SuperLU_688` - :ref:`list_software_supermagic_1072` - :ref:`list_software_supernova_995` - :ref:`list_software_SVDetect_770` - :ref:`list_software_SVDquest_799` - :ref:`list_software_swarm_554` - :ref:`list_software_SWASH_390` - :ref:`list_software_SWIG_314` - :ref:`list_software_SymEngine_911` - :ref:`list_software_sympy_578` - :ref:`list_software_Szip_422` .. _list_software_S-Lang_514: *S-Lang* ++++++++ S-Lang is a multi-platform programmer's library designed to allow a developer to create robust multi-platform software. It provides facilities required by interactive applications such as display/screen management, keyboard input, keymaps, and so on. *homepage*: http://www.jedsoft.org/slang/ ========= ============= version toolchain ========= ============= ``2.3.0`` ``GCC/4.9.2`` ========= ============= .. _list_software_S4_135: *S4* ++++ S4 stands for Stanford Stratified Structure Solver, a frequency domain code to solve the linear Maxwell’s equations in layered periodic structures. Internally, it uses Rigorous Coupled Wave Analysis (RCWA, also called the Fourier Modal Method (FMM)) and the S-matrix algorithm. *homepage*: https://web.stanford.edu/group/fan/S4 ================== ============== version toolchain ================== ============== ``1.1.1-20180610`` ``foss/2017b`` ================== ============== .. _list_software_SAGE_288: *SAGE* ++++++ S.A.G.E. (Statistical Analysis for Genetic Epidemiology) is free software package containing programs for use in the genetic analysis of family, pedigree and individual data. *homepage*: http://darwin.cwru.edu/sage/ ======= ========== version toolchain ======= ========== ``6.3`` ``system`` ``6.4`` ``system`` ======= ========== .. _list_software_Sailfish_819: *Sailfish* ++++++++++ Sailfish is a software tool that implements a novel, alignment-free algorithm for the estimation of isoform abundances directly from a set of reference sequences and RNA-seq reads. *homepage*: http://www.cs.cmu.edu/~ckingsf/software/sailfish/ ========== ================== ============== version versionsuffix toolchain ========== ================== ============== ``0.10.1`` ``-Python-2.7.12`` ``foss/2016b`` ========== ================== ============== .. _list_software_SALib_427: *SALib* +++++++ Sensitivity Analysis Library in Python (Numpy). Contains Sobol, Morris, Fractional Factorial and FAST methods. *homepage*: http://SALib.github.io/SALib/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.1.3`` ``-Python-2.7.14`` ``intel/2017b`` ========= ================== =============== .. _list_software_Salmon_618: *Salmon* ++++++++ Salmon is a wicked-fast program to produce a highly-accurate, transcript-level quantification estimates from RNA-seq data. *homepage*: https://github.com/COMBINE-lab/salmon ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``0.8.2`` ``system`` ``0.8.2`` ``-Python-2.7.12`` ``foss/2016b`` ``0.11.2`` ``intel/2018a`` ``0.12.0`` ``foss/2018b`` ``0.14.1`` ``foss/2018b`` ``0.14.2`` ``gompi/2019a`` ``1.0.0`` ``gompi/2019a`` ========== ================== =============== .. _list_software_SALMON-TDDFT_877: *SALMON-TDDFT* ++++++++++++++ SALMON is an open-source computer program for ab-initio quantum-mechanical calculations of electron dynamics at the nanoscale that takes place in various situations of light-matter interactions. It is based on time-dependent density functional theory, solving time-dependent Kohn-Sham equation in real time and real space with norm-conserving pseudopotentials. *homepage*: https://salmon-tddft.jp ========= =============================== version toolchain ========= =============================== ``1.2.1`` ``foss/2018b``, ``intel/2018b`` ========= =============================== .. _list_software_Sambamba_788: *Sambamba* ++++++++++ Sambamba is a high performance modern robust and fast tool (and library), written in the D programming language, for working with SAM and BAM files. Current functionality is an important subset of samtools functionality, including view, index, sort, markdup, and depth. *homepage*: https://lomereiter.github.io/sambamba/ ========= ========== version toolchain ========= ========== ``0.6.6`` ``system`` ``0.7.1`` ``system`` ========= ========== .. _list_software_Samcef_591: *Samcef* ++++++++ FEM solver solution suite for basic linear structures to advanced, flexible nonlinear mechanisms and thermal applications. *homepage*: http://www.plm.automation.siemens.com/en_us/products/lms/samtech/samcef-solver-suite/ =========== ========== version toolchain =========== ========== ``17.0-03`` ``system`` =========== ========== .. _list_software_samclip_745: *samclip* +++++++++ Filter SAM file for soft and hard clipped alignments *homepage*: https://github.com/tseemann/samclip ======= ================ ================= version versionsuffix toolchain ======= ================ ================= ``0.2`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` ======= ================ ================= .. _list_software_SAMtools_786: *SAMtools* ++++++++++ SAM Tools provide various utilities for manipulating alignments in the SAM format, including sorting, merging, indexing and generating alignments in a per-position format. *homepage*: http://www.htslib.org/ ========== ================= ======================================================================================================================================= version versionsuffix toolchain ========== ================= ======================================================================================================================================= ``0.1.17`` ``intel/2017a`` ``0.1.19`` ``foss/2016a``, ``foss/2016b`` ``0.1.20`` ``foss/2018b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ``1.2`` ``foss/2016b`` ``1.3`` ``foss/2016a``, ``intel/2016a`` ``1.3.1`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``1.3.1`` ``-HTSlib-1.3.2`` ``intel/2016b`` ``1.4`` ``foss/2016b``, ``intel/2016b``, ``intel/2017a`` ``1.4.1`` ``intel/2017a`` ``1.5`` ``foss/2016b``, ``intel/2017a`` ``1.6`` ``GCC/6.4.0-2.28``, ``foss/2017a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2017b`` ``1.7`` ``foss/2018a``, ``intel/2018a`` ``1.8`` ``intel/2018a`` ``1.9`` ``GCC/6.4.0-2.28``, ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1``, ``intel/2018b`` ``1.10`` ``GCC/8.2.0-2.31.1`` ========== ================= ======================================================================================================================================= .. _list_software_SAS_231: *SAS* +++++ SAS is a software suite for advanced analytics, multivariate analyses, business intelligence, data management, and predictive analytics. *homepage*: https://www.sas.com ======= ========== version toolchain ======= ========== ``9.4`` ``system`` ======= ========== .. _list_software_savvy_569: *savvy* +++++++ Interface to various variant calling formats. *homepage*: https://github.com/statgen/savvy ========= ==================== version toolchain ========= ==================== ``1.3.0`` ``GCC/8.2.0-2.31.1`` ========= ==================== .. _list_software_Saxon-HE_707: *Saxon-HE* ++++++++++ Open Source SAXON XSLT processor developed by Saxonica Limited. *homepage*: http://saxon.sourceforge.net ============ =================== ========== version versionsuffix toolchain ============ =================== ========== ``9.7.0.4`` ``-Java-1.7.0_79`` ``system`` ``9.7.0.21`` ``-Java-1.8.0_162`` ``system`` ============ =================== ========== .. _list_software_sbt_329: *sbt* +++++ sbt is a build tool for Scala, Java, and more. *homepage*: http://www.scala-sbt.org/ ========= =================== ========== version versionsuffix toolchain ========= =================== ========== ``1.0.2`` ``-Java-1.8.0_152`` ``system`` ========= =================== ========== .. _list_software_ScaLAPACK_707: *ScaLAPACK* +++++++++++ The ScaLAPACK (or Scalable LAPACK) library includes a subset of LAPACK routines redesigned for distributed memory MIMD parallel computers. *homepage*: https://www.netlib.org/scalapack/ ========= ================================= ============================================================================================================================================ version versionsuffix toolchain ========= ================================= ============================================================================================================================================ ``2.0.2`` ``gompi/2019b``, ``gompic/2019b`` ``2.0.2`` ``-OpenBLAS-0.2.13-LAPACK-3.5.0`` ``gmvapich2/1.7.20`` ``2.0.2`` ``-OpenBLAS-0.2.15-LAPACK-3.6.0`` ``gmpich/2016a``, ``gmvapich2/2016a``, ``gompi/2016a`` ``2.0.2`` ``-OpenBLAS-0.2.18-LAPACK-3.6.0`` ``gompi/2016.04``, ``gompi/2016.06`` ``2.0.2`` ``-OpenBLAS-0.2.18-LAPACK-3.6.1`` ``gompi/2016.07``, ``gompi/2016b`` ``2.0.2`` ``-OpenBLAS-0.2.19-LAPACK-3.6.1`` ``gompi/2016.09`` ``2.0.2`` ``-OpenBLAS-0.2.19-LAPACK-3.7.0`` ``gompi/2017a`` ``2.0.2`` ``-OpenBLAS-0.2.20`` ``gimpi/2017b``, ``gimpi/2018a``, ``gimpic/2017b``, ``gmpich/2017.08``, ``gompi/2017b``, ``gompi/2018a``, ``gompic/2017b``, ``gompic/2018a`` ``2.0.2`` ``-OpenBLAS-0.3.1`` ``gompi/2018b``, ``gompic/2018b`` ``2.0.2`` ``-OpenBLAS-0.3.3`` ``gompi/2018.08`` ``2.0.2`` ``-OpenBLAS-0.3.5`` ``gompi/2019a``, ``gompic/2019a`` ========= ================================= ============================================================================================================================================ .. _list_software_Scalasca_795: *Scalasca* ++++++++++ Scalasca is a software tool that supports the performance optimization of parallel programs by measuring and analyzing their runtime behavior. The analysis identifies potential performance bottlenecks -- in particular those concerning communication and synchronization -- and offers guidance in exploring their causes. *homepage*: https://www.scalasca.org/ ======= =============== version toolchain ======= =============== ``2.3`` ``foss/2016a`` ``2.5`` ``gompi/2019a`` ======= =============== .. _list_software_SCALCE_427: *SCALCE* ++++++++ SCALCE [skeɪlz] is a FASTQ compression tool that uses locally consistet parsing to obtain better compression rate. SCALCE has been specifically designed for Illumina reads but it can handle other technologies (that generate base pair reads) if the read length is the same throughout the file. *homepage*: http://scalce.sourceforge.net/Home ======= ============= version toolchain ======= ============= ``2.7`` ``GCC/4.8.2`` ======= ============= .. _list_software_sciClone_816: *sciClone* ++++++++++ An R package for inferring the subclonal architecture of tumors *homepage*: https://github.com/genome/sciclone ======= ============= ============== version versionsuffix toolchain ======= ============= ============== ``1.1`` ``-R-3.5.1`` ``foss/2018b`` ======= ============= ============== .. _list_software_ScientificPython_1667: *ScientificPython* ++++++++++++++++++ ScientificPython is a collection of Python modules for scientific computing. It contains support for geometry, mathematical functions, statistics, physical units, IO, visualization, and parallelization. *homepage*: https://sourcesup.cru.fr/projects/scientific-py/ ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``2.9.4`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ========= ================== =============================== .. _list_software_scikit-allel_1214: *scikit-allel* ++++++++++++++ This package provides utilities for exploratory analysis of large scale genetic variation data. It is based on numpy, scipy and other general-purpose Python scientific libraries. *homepage*: http://scikit-allel.readthedocs.io/en/latest/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.1.8`` ``-Python-2.7.13`` ``foss/2017a`` ========= ================== ============== .. _list_software_scikit-image_1207: *scikit-image* ++++++++++++++ scikit-image is a collection of algorithms for image processing. *homepage*: https://scikit-image.org/ ========== ================== =================================================== version versionsuffix toolchain ========== ================== =================================================== ``0.12.3`` ``-Python-2.7.11`` ``foss/2016a`` ``0.12.3`` ``-Python-2.7.12`` ``intel/2016b`` ``0.12.3`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` ``0.13.0`` ``-Python-2.7.13`` ``intel/2017a`` ``0.13.0`` ``-Python-3.6.1`` ``intel/2017a`` ``0.13.0`` ``-Python-3.6.3`` ``foss/2017b`` ``0.13.1`` ``-Python-2.7.14`` ``intel/2017b`` ``0.13.1`` ``-Python-3.6.3`` ``foss/2017b`` ``0.13.1`` ``-Python-3.6.4`` ``foss/2018a`` ``0.14.0`` ``-Python-3.6.4`` ``intel/2018a`` ``0.14.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``0.15.0`` ``-Python-3.7.2`` ``foss/2019a`` ``0.16.2`` ``-Python-3.7.4`` ``foss/2019b`` ========== ================== =================================================== .. _list_software_scikit-learn_1222: *scikit-learn* ++++++++++++++ Scikit-learn integrates machine learning algorithms in the tightly-knit scientific Python world, building upon numpy, scipy, and matplotlib. As a machine-learning module, it provides versatile tools for data mining and analysis in any field of science and engineering. It strives to be simple and efficient, accessible to everybody, and reusable in various contexts. *homepage*: https://scikit-learn.org/stable/index.html ========== ================================= ======================================================================== version versionsuffix toolchain ========== ================================= ======================================================================== ``0.16.1`` ``-Python-2.7.13`` ``foss/2017a`` ``0.17.1`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``0.17.1`` ``-Python-2.7.11-freetype-2.6.3`` ``intel/2016a`` ``0.17.1`` ``-Python-2.7.12`` ``intel/2016b`` ``0.17.1`` ``-Python-3.5.1`` ``foss/2016a``, ``intel/2016a`` ``0.18`` ``-Python-2.7.12`` ``intel/2016b`` ``0.18`` ``-Python-3.5.2`` ``intel/2016b`` ``0.18.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``0.18.1`` ``-Python-2.7.13`` ``intel/2017a`` ``0.18.1`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` ``0.18.1`` ``-Python-3.6.1`` ``intel/2017a`` ``0.18.2`` ``-Python-3.6.1`` ``intel/2017a`` ``0.19.0`` ``-Python-3.6.1`` ``intel/2017a`` ``0.19.1`` ``-Python-2.7.13`` ``foss/2017a`` ``0.19.1`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``0.19.1`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``0.19.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``0.20.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``0.20.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``0.20.2`` ``-Python-2.7.15`` ``foss/2018b`` ``0.20.2`` ``-Python-3.6.6`` ``foss/2018b`` ``0.20.3`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a`` ``0.21.3`` ``-Python-3.7.4`` ``foss/2019b``, ``intel/2019b`` ========== ================================= ======================================================================== .. _list_software_scikit-multilearn_1777: *scikit-multilearn* +++++++++++++++++++ Scikit-multilearn is a BSD-licensed library for multi-label classification that is built on top of the well-known scikit-learn ecosystem. *homepage*: http://scikit.ml ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``0.2.0`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== .. _list_software_scikit-optimize_1573: *scikit-optimize* +++++++++++++++++ Scikit-Optimize, or skopt, is a simple and efficient library to minimize (very) expensive and noisy black-box functions. *homepage*: https://scikit-optimize.github.io ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``0.5.2`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================= =============== .. _list_software_SCIPhI_480: *SCIPhI* ++++++++ Single-cell mutation identification via phylogenetic inference (SCIPhI) is a new approach to mutation detection in individual tumor cells by leveraging the evolutionary relationship among cells. *homepage*: https://github.com/cbg-ethz/SCIPhI ========= =============== version toolchain ========= =============== ``0.1.3`` ``intel/2018b`` ========= =============== .. _list_software_scipy_552: *scipy* +++++++ SciPy is a collection of mathematical algorithms and convenience functions built on the Numpy extension for Python. *homepage*: http://www.scipy.org ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``0.16.0`` ``-Python-2.7.12`` ``intel/2016b`` ``0.17.0`` ``-Python-2.7.11`` ``intel/2016a`` ``0.19.0`` ``-Python-3.5.2`` ``intel/2016b`` ========== ================== =============== .. _list_software_SciPy-bundle_1167: *SciPy-bundle* ++++++++++++++ Bundle of Python packages for scientific software *homepage*: https://python.org/ =========== ================== ======================================================================== version versionsuffix toolchain =========== ================== ======================================================================== ``2019.03`` ``foss/2019a``, ``fosscuda/2019a``, ``intel/2019a``, ``intelcuda/2019a`` ``2019.10`` ``-Python-2.7.16`` ``foss/2019b`` ``2019.10`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b``, ``intel/2019b`` =========== ================== ======================================================================== .. _list_software_SCnorm_594: *SCnorm* ++++++++ This package implements SCnorm — a method to normalize single-cell RNA-seq data. *homepage*: https://bioconductor.org/packages/SCnorm ========== ============= =============== version versionsuffix toolchain ========== ============= =============== ``0.99.7`` ``-R-3.4.0`` ``intel/2017a`` ========== ============= =============== .. _list_software_Scoary_625: *Scoary* ++++++++ Microbial pan-GWAS using the output from Roary *homepage*: https://github.com/AdmiralenOla/Scoary ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``1.6.16`` ``-Python-2.7.14`` ``intel/2018a`` ========== ================== =============== .. _list_software_SCons_486: *SCons* +++++++ SCons is a software construction tool. *homepage*: https://www.scons.org/ ========= ======================= ================================================================================= version versionsuffix toolchain ========= ======================= ================================================================================= ``2.4.1`` ``-Python-2.7.11`` ``foss/2016a`` ``2.5.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``2.5.1`` ``intel/2017a`` ``2.5.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``2.5.1`` ``-Python-2.7.13`` ``intel/2017a`` ``3.0.1`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a``, ``iomkl/2018a`` ``3.0.1`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``3.0.1`` ``-Python-2.7.15-bare`` ``GCCcore/7.3.0`` ``3.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``3.0.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``3.0.4`` ``-Python-2.7.15`` ``foss/2018b`` ``3.0.5`` ``GCCcore/8.2.0`` ``3.0.5`` ``-Python-2.7.15`` ``GCCcore/8.2.0`` ``3.0.5`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``3.1.1`` ``GCCcore/8.3.0`` ========= ======================= ================================================================================= .. _list_software_SCOOP_388: *SCOOP* +++++++ SCOOP (Scalable COncurrent Operations in Python) is a distributed task module allowing concurrent parallel programming on various environments, from heterogeneous grids to supercomputers. *homepage*: http://code.google.com/p/scoop/ =========== ================== ================= version versionsuffix toolchain =========== ================== ================= ``0.6.2`` ``-Python-2.7.12`` ``intel/2016b`` ``0.7.1.1`` ``GCCcore/8.2.0`` ``0.7.1.1`` ``-Python-2.7.11`` ``intel/2016a`` ``0.7.1.1`` ``-Python-2.7.14`` ``intel/2017b`` ``0.7.1.1`` ``-Python-3.5.1`` ``intel/2016a`` =========== ================== ================= .. _list_software_Score-P_633: *Score-P* +++++++++ The Score-P measurement infrastructure is a highly scalable and easy-to-use tool suite for profiling, event tracing, and online analysis of HPC applications. *homepage*: https://www.score-p.org ========= =============== version toolchain ========= =============== ``2.0.1`` ``foss/2016a`` ``6.0`` ``gompi/2019a`` ========= =============== .. _list_software_SCOTCH_452: *SCOTCH* ++++++++ Software package and libraries for sequential and parallel graph partitioning, static mapping, and sparse matrix block ordering, and sequential mesh and hypergraph partitioning. *homepage*: https://gforge.inria.fr/projects/scotch/ =================== ============= ===================================================================================================================================================== version versionsuffix toolchain =================== ============= ===================================================================================================================================================== ``5.1.12b_esmumps`` ``foss/2017b`` ``6.0.4`` ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``6.0.4`` ``-64bitint`` ``foss/2017b`` ``6.0.6`` ``foss/2018a``, ``foss/2018b``, ``gompi/2019a``, ``iimpi/2019a``, ``intel/2018a`` ``6.0.9`` ``gompi/2019b``, ``iimpi/2019b`` =================== ============= ===================================================================================================================================================== .. _list_software_scp_326: *scp* +++++ The scp.py module uses a paramiko transport to send and recieve files via the scp1 protocol. *homepage*: https://github.com/jbardin/scp.py ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``0.10.2`` ``-Python-2.7.12`` ``intel/2016b`` ``0.13.1`` ``-Python-2.7.15`` ``intel/2018b`` ``0.13.2`` ``-Python-2.7.15`` ``intel/2018b`` ========== ================== =============== .. _list_software_Scrappie_823: *Scrappie* ++++++++++ Scrappie is a technology demonstrator for the Oxford Nanopore Research Algorithms group. *homepage*: https://github.com/nanoporetech/scrappie ========= =============== version toolchain ========= =============== ``1.3.2`` ``intel/2018a`` ========= =============== .. _list_software_SDCC_285: *SDCC* ++++++ SDCC is a retargettable, optimizing ANSI - C compiler suite that targets the Intel MCS51 based microprocessors (8031, 8032, 8051, 8052, etc.), Maxim (formerly Dallas) DS80C390 variants, Freescale (formerly Motorola) HC08 based (hc08, s08) and Zilog Z80 based MCUs (z80, z180, gbz80, Rabbit 2000/3000, Rabbit 3000A). Work is in progress on supporting the Microchip PIC16 and PIC18 targets. It can be retargeted for other microprocessors. *homepage*: http://sdcc.sourceforge.net/ ========= ========== version toolchain ========= ========== ``3.3.0`` ``system`` ========= ========== .. _list_software_SDL2_277: *SDL2* ++++++ SDL: Simple DirectMedia Layer, a cross-platform multimedia library *homepage*: http://www.libsdl.org/ ========= ====================================================================== version toolchain ========= ====================================================================== ``2.0.4`` ``intel/2016b`` ``2.0.8`` ``foss/2017b``, ``intel/2017b``, ``intel/2018a`` ``2.0.9`` ``GCCcore/8.2.0``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ========= ====================================================================== .. _list_software_Seaborn_714: *Seaborn* +++++++++ Seaborn is a Python visualization library based on matplotlib. It provides a high-level interface for drawing attractive statistical graphics. *homepage*: http://stanford.edu/~mwaskom/software/seaborn/ ========= ================== ========================================================================================= version versionsuffix toolchain ========= ================== ========================================================================================= ``0.7.1`` ``-Python-2.7.12`` ``intel/2016b`` ``0.8.1`` ``-Python-2.7.13`` ``foss/2017a`` ``0.8.1`` ``-Python-2.7.14`` ``intel/2018a`` ``0.9.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018a``, ``intelcuda/2017b`` ``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` ``0.9.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``0.9.0`` ``-Python-3.6.4`` ``intel/2018a`` ``0.9.0`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``0.9.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ========= ================== ========================================================================================= .. _list_software_SearchGUI_827: *SearchGUI* +++++++++++ SearchGUI is a user-friendly open-source graphical user interface for configuring and running proteomics identification search engines and de novo sequencing algorithms, currently supporting X! Tandem, MS-GF+, MS Amanda, MyriMatch, Comet, Tide, Andromeda, OMSSA, Novor and DirecTag. *homepage*: https://github.com/compomics/searchgui ========= =================== ========== version versionsuffix toolchain ========= =================== ========== ``3.3.3`` ``-Java-1.8.0_152`` ``system`` ========= =================== ========== .. _list_software_segemehl_842: *segemehl* ++++++++++ segemehl is a software to map short sequencer reads to reference genomes. Unlike other methods, segemehl is able to detect not only mismatches but also insertions and deletions. Furthermore, segemehl is not limited to a specific read length and is able to mapprimer- or polyadenylation contaminated reads correctly. segemehl implements a matching strategy based on enhanced suffix arrays (ESA). Segemehl now supports the SAM format, reads gziped queries to save both disk and memory space and allows bisulfite sequencing mapping and split read mapping. *homepage*: http://www.bioinf.uni-leipzig.de/Software/segemehl/ ========= ================================================ version toolchain ========= ================================================ ``0.2.0`` ``foss/2016b``, ``intel/2017b``, ``intel/2018a`` ``0.3.4`` ``foss/2018b`` ========= ================================================ .. _list_software_SelEstim_806: *SelEstim* ++++++++++ SelEstim is aimed at distinguishing neutral from selected polymorphisms and estimate the intensity of selection at the latter. The SelEstim model accounts explicitly for positive selection, and it is assumed that all marker loci in the dataset are responding to selection, to some extent *homepage*: http://www1.montpellier.inra.fr/CBGP/software/selestim/index.html ========= ================= ========== version versionsuffix toolchain ========= ================= ========== ``1.1.4`` ``-Linux-64bits`` ``system`` ========= ================= ========== .. _list_software_sep_328: *sep* +++++ Python and C library for Source Extraction and Photometry. (this easyconfig provides python library only) *homepage*: https://sep.readthedocs.io ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``1.0.3`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ========= ================== =============================== .. _list_software_Seq-Gen_624: *Seq-Gen* +++++++++ Seq-Gen is a program that will simulate the evolution of nucleotide or amino acid sequences along a phylogeny, using common models of the substitution process. *homepage*: http://tree.bio.ed.ac.uk/software/Seq-Gen ========= =============== version toolchain ========= =============== ``1.3.4`` ``intel/2017b`` ========= =============== .. _list_software_seq2HLA_592: *seq2HLA* +++++++++ In-silico method written in Python and R to determine HLA genotypes of a sample. *homepage*: https://github.com/TRON-Bioinformatics/seq2HLA ======= ================== =============== version versionsuffix toolchain ======= ================== =============== ``2.3`` ``-Python-2.7.14`` ``intel/2018a`` ``2.3`` ``-Python-2.7.15`` ``foss/2018b`` ======= ================== =============== .. _list_software_SeqAn_472: *SeqAn* +++++++ SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data *homepage*: https://www.seqan.de/ ========= ===================================================== version toolchain ========= ===================================================== ``2.3.2`` ``foss/2016b`` ``2.4.0`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``intel/2018b`` ========= ===================================================== .. _list_software_SeqAn3_523: *SeqAn3* ++++++++ SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance. *homepage*: https://github.com/seqan/seqan3 ========= ========== version toolchain ========= ========== ``3.0.0`` ``system`` ========= ========== .. _list_software_Seqmagick_917: *Seqmagick* +++++++++++ We often have to convert between sequence formats and do little tasks on them, and it's not worth writing scripts for that. Seqmagick is a kickass little utility built in the spirit of imagemagick to expose the file format conversion in Biopython in a convenient way. Instead of having a big mess of scripts, there is one that takes arguments. *homepage*: https://fhcrc.github.io/seqmagick/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``0.6.1`` ``-Python-2.7.11`` ``foss/2016a`` ``0.6.2`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== ============== .. _list_software_SeqPrep_704: *SeqPrep* +++++++++ Tool for stripping adaptors and/or merging paired reads with overlap into single reads. *homepage*: https://github.com/jstjohn/SeqPrep ========= ================= version toolchain ========= ================= ``1.3.2`` ``GCCcore/7.3.0`` ========= ================= .. _list_software_seqtk_552: *seqtk* +++++++ Seqtk is a fast and lightweight tool for processing sequences in the FASTA or FASTQ format. It seamlessly parses both FASTA and FASTQ files which can also be optionally compressed by gzip. *homepage*: https://github.com/lh3/seqtk/ ======= ==================================================== version toolchain ======= ==================================================== ``1.2`` ``foss/2016b``, ``intel/2017a`` ``1.3`` ``GCC/8.2.0-2.31.1``, ``foss/2018a``, ``foss/2018b`` ======= ==================================================== .. _list_software_Serf_400: *Serf* ++++++ The serf library is a high performance C-based HTTP client library built upon the Apache Portable Runtime (APR) library *homepage*: http://serf.apache.org/ ========= ====================================================================================== version toolchain ========= ====================================================================================== ``1.3.9`` ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2017b``, ``intel/2017b``, ``iomkl/2018a`` ========= ====================================================================================== .. _list_software_setuptools_1122: *setuptools* ++++++++++++ Easily download, build, install, upgrade, and uninstall Python packages *homepage*: https://pypi.org/project/setuptools ========== ============= ========== version versionsuffix toolchain ========== ============= ========== ``1.4.2`` ``system`` ``41.0.1`` ``-py3`` ``system`` ========== ============= ========== .. _list_software_Seurat_628: *Seurat* ++++++++ Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data. *homepage*: http://satijalab.org/seurat ============ ============= =============== version versionsuffix toolchain ============ ============= =============== ``1.4.0.16`` ``-R-3.4.0`` ``intel/2017a`` ``2.3.4`` ``-R-3.4.4`` ``intel/2018a`` ``2.3.4`` ``-R-3.5.1`` ``foss/2018b`` ============ ============= =============== .. _list_software_Shannon_725: *Shannon* +++++++++ Shannon is a program for assembling transcripts from RNA-Seq data *homepage*: https://sreeramkannan.github.io/Shannon/ ============ ================== =============== version versionsuffix toolchain ============ ================== =============== ``20170511`` ``-Python-2.7.13`` ``intel/2017a`` ============ ================== =============== .. _list_software_shapAAR_640: *shapAAR* +++++++++ An R package for the extraction, analysis and classification of (not only) archaeological objects from scanned images. *homepage*: https://github.com/ISAAKiel/shapAAR ================== ============= ============== version versionsuffix toolchain ================== ============= ============== ``0.1.0-20180425`` ``-R-3.6.0`` ``foss/2019a`` ================== ============= ============== .. _list_software_SHAPEIT_526: *SHAPEIT* +++++++++ SHAPEIT is a fast and accurate method for estimation of haplotypes (aka phasing) from genotype or sequencing data. *homepage*: https://mathgen.stats.ox.ac.uk/genetics_software/shapeit/shapeit.html ========== =============== ========== version versionsuffix toolchain ========== =============== ========== ``2.r837`` ``.GLIBCv2.12`` ``system`` ``2.r904`` ``.glibcv2.17`` ``system`` ========== =============== ========== .. _list_software_sharutils_991: *sharutils* +++++++++++ GNU shar makes so-called shell archives out of many files, preparing them for transmission by electronic mail services, while unshar helps unpacking shell archives after reception. *homepage*: https://www.gnu.org/software/sharutils/ ======== ================= version toolchain ======== ================= ``4.15`` ``GCCcore/6.3.0`` ======== ================= .. _list_software_shift_542: *shift* +++++++ Shift is a framework for Self-Healing Independent File Transfer that provides high performance and resilience for local and remote transfers through a variety of techniques. *homepage*: http://people.nas.nasa.gov/~kolano/projects/shift.html ======= =============== version toolchain ======= =============== ``4.0`` ``intel/2016a`` ======= =============== .. _list_software_SHORE_385: *SHORE* +++++++ SHORE, for Short Read, is a mapping and analysis pipeline for short read data produced on the Illumina platform. *homepage*: http://1001genomes.org/software/shore.html ========= ============== version toolchain ========= ============== ``0.9.3`` ``foss/2016a`` ========= ============== .. _list_software_Short-Pair_969: *Short-Pair* ++++++++++++ Sensitive Short Read Homology Search for Paired-End Reads *homepage*: https://sourceforge.net/projects/short-pair ============ ================== ============== version versionsuffix toolchain ============ ================== ============== ``20170125`` ``-Python-2.7.15`` ``foss/2018b`` ============ ================== ============== .. _list_software_shovill_769: *shovill* +++++++++ Faster SPAdes assembly of Illumina reads *homepage*: https://github.com/tseemann/shovill ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``0.9.0`` ``-Python-2.7.14`` ``foss/2018a`` ``1.0.4`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== ============== .. _list_software_shrinkwrap_1097: *shrinkwrap* ++++++++++++ A std::streambuf wrapper for compression formats. *homepage*: https://github.com/jonathonl/shrinkwrap ============== ================= version toolchain ============== ================= ``1.0.0-beta`` ``GCCcore/8.2.0`` ============== ================= .. _list_software_Sibelia_697: *Sibelia* +++++++++ Sibelia: A comparative genomics tool: It assists biologists in analysing the genomic variations that correlate with pathogens, or the genomic changes that help microorganisms adapt in different environments. Sibelia will also be helpful for the evolutionary and genome rearrangement studies for multiple strains of microorganisms. *homepage*: http://bioinf.spbau.ru/en/sibelia ========= ============== version toolchain ========= ============== ``3.0.6`` ``foss/2016b`` ``3.0.7`` ``foss/2018b`` ========= ============== .. _list_software_sickle_635: *sickle* ++++++++ Windowed Adaptive Trimming for fastq files using quality *homepage*: https://github.com/najoshi/sickle ======== =============================== version toolchain ======== =============================== ``1.33`` ``foss/2017a``, ``intel/2018a`` ======== =============================== .. _list_software_Siesta_617: *Siesta* ++++++++ SIESTA is both a method and its computer program implementation, to perform efficient electronic structure calculations and ab initio molecular dynamics simulations of molecules and solids. *homepage*: http://departments.icmab.es/leem/siesta ========== =============================== version toolchain ========== =============================== ``4.0`` ``intel/2017a`` ``4.0.1`` ``intel/2017a`` ``4.1-b2`` ``intel/2017a`` ``4.1-b3`` ``intel/2017a`` ``4.1-b4`` ``foss/2018b``, ``intel/2018b`` ========== =============================== .. _list_software_SimPEG_517: *SimPEG* ++++++++ Simulation and Parameter Estimation in Geophysics: a python package for simulation and gradient based parameter estimation in the context of geophysical applications. *homepage*: http://simpeg.xyz ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.3.1`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== .. _list_software_SIMPLE_458: *SIMPLE* ++++++++ Single-particle IMage Processing Linux Engine is a program package for cryo-EM image processing, focusing on ab initio 3D reconstruction of low-symmetry single-particles. *homepage*: http://simplecryoem.com/ ======= ============== version toolchain ======= ============== ``2.5`` ``foss/2018a`` ======= ============== .. _list_software_SimpleElastix_1348: *SimpleElastix* +++++++++++++++ Multi-lingual medical image registration library. *homepage*: http://simpleelastix.github.io/ ========== ================= ============== version versionsuffix toolchain ========== ================= ============== ``0.10.0`` ``-Python-3.6.3`` ``foss/2017b`` ``0.10.0`` ``-Python-3.6.4`` ``foss/2018a`` ========== ================= ============== .. _list_software_SimpleITK_850: *SimpleITK* +++++++++++ imbalanced-learn is a Python package offering a number of re-sampling techniques commonly used in datasets showing strong between-class imbalance. *homepage*: https://github.com/scikit-learn-contrib/imbalanced-learn ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.1.0`` ``-Python-2.7.15`` ``foss/2018b`` ``1.1.0`` ``-Python-3.6.4`` ``foss/2018a`` ``1.1.0`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================== ============== .. _list_software_simpy_562: *simpy* +++++++ SimPy is a process-based discrete-event simulation framework based on standard Python. *homepage*: https://simpy.readthedocs.io ========== ================= =============== version versionsuffix toolchain ========== ================= =============== ``3.0.11`` ``intel/2019a`` ``3.0.11`` ``-Python-3.6.6`` ``intel/2018b`` ========== ================= =============== .. _list_software_SimVascular_1130: *SimVascular* +++++++++++++ SimVascular is an open source software suite for cardiovascular simulation, providing a complete pipeline from medical image data to 3D model construction, meshing, and blood flow simulation. *homepage*: http://simvascular.github.io/ ============= =============== version toolchain ============= =============== ``2.16.0406`` ``intel/2016b`` ============= =============== .. _list_software_SingleM_687: *SingleM* +++++++++ SingleM is a tool to find the abundances of discrete operational taxonomic units (OTUs) directly from shotgun metagenome data, without heavy reliance on reference sequence databases. *homepage*: https://github.com/wwood/singlem ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``0.12.1`` ``-Python-2.7.15`` ``intel/2019a`` ========== ================== =============== .. _list_software_Singularity_1179: *Singularity* +++++++++++++ Singularity is a portable application stack packaging and runtime utility. *homepage*: http://singularity.lbl.gov ========= ================== version toolchain ========= ================== ``1.0`` ``GCC/4.9.3-2.25`` ``2.2.1`` ``GCC/6.3.0-2.27`` ``2.3.1`` ``GCC/5.4.0-2.26`` ``2.4.2`` ``GCC/5.4.0-2.26`` ========= ================== .. _list_software_SIONlib_624: *SIONlib* +++++++++ SIONlib is a scalable I/O library for parallel access to task-local files. The library not only supports writing and reading binary data to or from several thousands of processors into a single or a small number of physical files, but also provides global open and close functions to access SIONlib files in parallel. This package provides a stripped-down installation of SIONlib for use with performance tools (e.g., Score-P), with renamed symbols to avoid conflicts when an application using SIONlib itself is linked against a tool requiring a different SIONlib version. *homepage*: http://www.fz-juelich.de/ias/jsc/EN/Expertise/Support/Software/SIONlib/_node.html ========= ============= ================= version versionsuffix toolchain ========= ============= ================= ``1.6.1`` ``foss/2016a`` ``1.6.1`` ``-tools`` ``foss/2016a`` ``1.7.1`` ``foss/2017a`` ``1.7.1`` ``-tools`` ``foss/2017a`` ``1.7.4`` ``-tools`` ``GCCcore/8.2.0`` ========= ============= ================= .. _list_software_SIP_236: *SIP* +++++ SIP is a tool that makes it very easy to create Python bindings for C and C++ libraries. *homepage*: http://www.riverbankcomputing.com/software/sip/ =========== ================== =============================================== version versionsuffix toolchain =========== ================== =============================================== ``4.18`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``4.18.1`` ``-Python-2.7.11`` ``foss/2016a`` ``4.18.1`` ``-Python-2.7.12`` ``intel/2016b`` ``4.19`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``4.19.2`` ``-Python-2.7.13`` ``intel/2017a`` ``4.19.8`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b`` ``4.19.8`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``4.19.13`` ``-Python-2.7.15`` ``fosscuda/2018b`` =========== ================== =============================================== .. _list_software_SKESA_375: *SKESA* +++++++ SKESA is a de-novo sequence read assembler for cultured single isolate genomes based on DeBruijn graphs. *homepage*: https://github.com/ncbi/SKESA ========= ============== version toolchain ========= ============== ``2.2`` ``foss/2018a`` ``2.3.0`` ``foss/2018b`` ========= ============== .. _list_software_sketchmap_960: *sketchmap* +++++++++++ Sketch-map is a dimensionality reduction algorithm that is particularly well suited to examining the high-dimensionality data that is routinely produced in atomistic simulations. *homepage*: http://sketchmap.org/ ============ =============== version toolchain ============ =============== ``20170130`` ``intel/2016b`` ============ =============== .. _list_software_skewer_657: *skewer* ++++++++ skewer implements the bit-masked k-difference matching algorithm dedicated to the task of adapter trimming and it is specially designed for processing next-generation sequencing (NGS) paired-end sequences. *homepage*: https://github.com/relipmoc/skewer ========= =============== version toolchain ========= =============== ``0.2.2`` ``intel/2016b`` ========= =============== .. _list_software_SLEPc_407: *SLEPc* +++++++ SLEPc (Scalable Library for Eigenvalue Problem Computations) is a software library for the solution of large scale sparse eigenvalue problems on parallel computers. It is an extension of PETSc and can be used for either standard or generalized eigenproblems, with real or complex arithmetic. It can also be used for computing a partial SVD of a large, sparse, rectangular matrix, and to solve quadratic eigenvalue problems. *homepage*: http://www.grycap.upv.es/slepc/ ========== ============== version toolchain ========== ============== ``3.8.3`` ``foss/2017b`` ``3.9.2`` ``foss/2018a`` ``3.11.0`` ``foss/2018b`` ========== ============== .. _list_software_slepc4py_820: *slepc4py* ++++++++++ Python bindings for SLEPc, the Scalable Library for Eigenvalue Problem Computations. *homepage*: https://bitbucket.org/slepc/slepc4py ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``3.9.0`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================= ============== .. _list_software_sleuth_661: *sleuth* ++++++++ Investigate RNA-Seq transcript abundance from kallisto and perform differential expression analysis. *homepage*: http://pachterlab.github.io/sleuth ========== ============= =============== version versionsuffix toolchain ========== ============= =============== ``0.29.0`` ``-R-3.4.0`` ``intel/2017a`` ``0.30.0`` ``-R-3.5.1`` ``foss/2018b`` ========== ============= =============== .. _list_software_slidingwindow_1410: *slidingwindow* +++++++++++++++ slidingwindow is a simple little Python library for computing a set of windows into a larger dataset, designed for use with image-processing algorithms that utilise a sliding window to break the processing up into a series of smaller chunks. *homepage*: https://github.com/adamrehn/slidingwindow ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``0.0.13`` ``-Python-2.7.15`` ``intel/2018b`` ``0.0.13`` ``-Python-3.6.6`` ``intel/2018b`` ========== ================== =============== .. _list_software_smafa_520: *smafa* +++++++ Smafa attempts to align or cluster pre-aligned biological sequences, handling sequences which are all the same length. *homepage*: https://github.com/wwood/smafa ========= ================= version toolchain ========= ================= ``0.4.0`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_smallgenomeutilities_2160: *smallgenomeutilities* ++++++++++++++++++++++ The smallgenomeutilities are a collection of scripts that is useful for dealing and manipulating NGS data of small viral genomes. They are written in Python 3 with a small number of dependencies. *homepage*: https://github.com/cbg-ethz/smallgenomeutilities ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``0.2.1`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== .. _list_software_SMARTdenovo_1042: *SMARTdenovo* +++++++++++++ SMARTdenovo is a de novo assembler for PacBio and Oxford Nanopore (ONT) data. It produces an assembly from all-vs-all raw read alignments without an error correction stage. It also provides tools to generate accurate consensus sequences, though a platform dependent consensus polish tools (e.g. Quiver for PacBio or Nanopolish for ONT) are still required for higher accuracy. *homepage*: https://github.com/ruanjue/smartdenovo ============ ============== version toolchain ============ ============== ``20180219`` ``foss/2018b`` ============ ============== .. _list_software_Smoldyn_742: *Smoldyn* +++++++++ Smoldyn is a computer program for cell-scale biochemical simulations. It simulates each molecule of interest individually to capture natural stochasticity and to yield nanometer-scale spatial resolution. It treats other molecules implicitly, enabling it to simulate hundreds of thousands of molecules over several minutes of real time. Simulated molecules diffuse, react, are confined by surfaces, and bind to membranes much as they would in a real biological system. *homepage*: http://www.smoldyn.org/ ======== ============== version toolchain ======== ============== ``2.48`` ``foss/2016a`` ======== ============== .. _list_software_SMRT-Link_769: *SMRT-Link* +++++++++++ PacBio’s open-source SMRT Analysis software suite is designed for use with Single Molecule, Real-Time (SMRT) Sequencing data. You can analyze, visualize, and manage your data through an intuitive GUI or command-line interface. You can also integrate SMRT Analysis in your existing data workflow through the extensive set of APIs provided *homepage*: https://www.pacb.com/support/software-downloads/ =============== =================== ========== version versionsuffix toolchain =============== =================== ========== ``5.1.0.26412`` ``-cli-tools-only`` ``system`` ``6.0.0.47841`` ``-cli-tools-only`` ``system`` =============== =================== ========== .. _list_software_snakemake_944: *snakemake* +++++++++++ The Snakemake workflow management system is a tool to create reproducible and scalable data analyses. *homepage*: https://snakemake.readthedocs.io ========= ================= =============================== version versionsuffix toolchain ========= ================= =============================== ``5.2.2`` ``-Python-3.6.4`` ``intel/2018a`` ``5.2.4`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``5.7.1`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================= =============================== .. _list_software_SNAP_306: *SNAP* ++++++ SNAP is a general purpose gene finding program suitable for both eukaryotic and prokaryotic genomes. SNAP is an acroynm for Semi-HMM-based Nucleic Acid Parser. *homepage*: http://korflab.ucdavis.edu/software.html ============== ========================================================================= version toolchain ============== ========================================================================= ``1.0beta.23`` ``intel/2017b`` ``2013-11-29`` ``GCC/6.4.0-2.28``, ``GCC/8.3.0``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ============== ========================================================================= .. _list_software_SNAPE-pooled_1063: *SNAPE-pooled* ++++++++++++++ SNAPE-pooled computes the probability distribution for the frequency of the minor allele in a certain population, at a certain position in the genome. *homepage*: https://code.google.com/archive/p/snape-pooled/ ======= ============== version toolchain ======= ============== ``r32`` ``foss/2016a`` ======= ============== .. _list_software_snaphu_655: *snaphu* ++++++++ SNAPHU is an implementation of the Statistical-cost, Network-flow Algorithm for Phase Unwrapping proposed by Chen and Zebker *homepage*: https://web.stanford.edu/group/radar/softwareandlinks/sw/snaphu/ ========= =================================================== version toolchain ========= =================================================== ``1.4.2`` ``GCCcore/6.3.0``, ``intel/2016b``, ``intel/2017a`` ========= =================================================== .. _list_software_snappy_667: *snappy* ++++++++ Snappy is a compression/decompression library. It does not aim for maximum compression, or compatibility with any other compression library; instead, it aims for very high speeds and reasonable compression. *homepage*: https://github.com/google/snappy ========= ============================================================================================================ version toolchain ========= ============================================================================================================ ``1.1.2`` ``GCC/4.9.2`` ``1.1.3`` ``GCC/4.9.3``, ``GCC/4.9.3-2.25`` ``1.1.6`` ``system`` ``1.1.7`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``intel/2017a``, ``intel/2017b`` ========= ============================================================================================================ .. _list_software_snippy_675: *snippy* ++++++++ Snippy finds SNPs between a haploid reference genome and your NGS sequence reads. It will find both substitutions (snps) and insertions/deletions (indels). Rapid haploid variant calling and core genome alignment. *homepage*: https://github.com/tseemann/snippy ========= ================ ============== version versionsuffix toolchain ========= ================ ============== ``4.4.1`` ``-Perl-5.28.0`` ``foss/2018b`` ========= ================ ============== .. _list_software_snpEff_610: *snpEff* ++++++++ SnpEff is a variant annotation and effect prediction tool. It annotates and predicts the effects of genetic variants (such as amino acid changes). *homepage*: http://sourceforge.net/projects/snpeff/ ======== ================== ========== version versionsuffix toolchain ======== ================== ========== ``3.6`` ``-Java-1.7.0_80`` ``system`` ``4.1d`` ``-Java-1.7.0_80`` ``system`` ======== ================== ========== .. _list_software_SNPhylo_685: *SNPhylo* +++++++++ SNPhylo: a pipeline to generate a phylogenetic tree from huge SNP data *homepage*: http://chibba.pgml.uga.edu/snphylo/ ============ ========================== =============================== version versionsuffix toolchain ============ ========================== =============================== ``20140701`` ``foss/2016a``, ``intel/2016a`` ``20160204`` ``-Python-2.7.14-R-3.4.3`` ``foss/2017b``, ``intel/2017b`` ============ ========================== =============================== .. _list_software_SOAPaligner_1045: *SOAPaligner* +++++++++++++ SOAPaligner/soap2 is a member of the SOAP (Short Oligonucleotide Analysis Package). It is an updated version of SOAP software for short oligonucleotide alignment. *homepage*: http://soap.genomics.org.cn/soapaligner.html ======== ================= ========== version versionsuffix toolchain ======== ================= ========== ``2.21`` ``_Linux-x86_64`` ``system`` ======== ================= ========== .. _list_software_SOAPdenovo-Trans_1523: *SOAPdenovo-Trans* ++++++++++++++++++ SOAPdenovo-Trans is a de novo transcriptome assembler basing on the SOAPdenovo framework, adapt to alternative splicing and different expression level among transcripts. *homepage*: http://soap.genomics.org.cn/SOAPdenovo-Trans.html ========= =============== version toolchain ========= =============== ``1.0.4`` ``intel/2017a`` ========= =============== .. _list_software_SOAPdenovo2_1008: *SOAPdenovo2* +++++++++++++ SOAPdenovo is a novel short-read assembly method that can build a de novo draft assembly for human-sized genomes. The program is specially designed to assemble Illumina short reads. It creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way. SOAPdenovo2 is the successor of SOAPdenovo. *homepage*: http://soap.genomics.org.cn/index.html ======== =========================================================================================== version toolchain ======== =========================================================================================== ``r240`` ``GCC/5.4.0-2.26`` ``r241`` ``GCC/6.4.0-2.28``, ``foss/2018a``, ``iccifort/2017.4.196-GCC-6.4.0-2.28``, ``intel/2018a`` ======== =========================================================================================== .. _list_software_SOAPfuse_742: *SOAPfuse* ++++++++++ SOAPfuse is an open source tool developed for genome-wide detection of fusion transcripts from paired-end RNA-Seq data. *homepage*: https://sourceforge.net/p/soapfuse/wiki/Home/ ======== ================ ============== version versionsuffix toolchain ======== ================ ============== ``1.27`` ``-Perl-5.24.0`` ``foss/2016b`` ``1.27`` ``-Perl-5.28.0`` ``foss/2018b`` ======== ================ ============== .. _list_software_socat_538: *socat* +++++++ socat is a relay for bidirectional data transfer between two independent data channels. *homepage*: http://www.dest-unreach.org/socat =========== ================= version toolchain =========== ================= ``1.7.3.3`` ``GCCcore/8.2.0`` =========== ================= .. _list_software_SolexaQA++_852: *SolexaQA++* ++++++++++++ SolexaQA calculates sequence quality statistics and creates visual representations of data quality for second-generation sequencing data. Originally developed for the Illumina system (historically known as “Solexa”), SolexaQA now also supports Ion Torrent and 454 data. *homepage*: http://solexaqa.sourceforge.net ========= ============== version toolchain ========= ============== ``3.1.5`` ``foss/2016b`` ========= ============== .. _list_software_SortMeRNA_827: *SortMeRNA* +++++++++++ SortMeRNA is a biological sequence analysis tool for filtering, mapping and OTU-picking NGS reads. *homepage*: http://bioinfo.lifl.fr/RNA/sortmerna/ ======= ============== version toolchain ======= ============== ``2.1`` ``foss/2016a`` ======= ============== .. _list_software_Spack_498: *Spack* +++++++ Spack is a package manager for supercomputers, Linux, and macOS. It makes installing scientific software easy. With Spack, you can build a package with multiple versions, configurations, platforms, and compilers, and all of these builds can coexist on the same machine. *homepage*: https://spack.io/ ========== ========== version toolchain ========== ========== ``0.10.0`` ``system`` ``0.11.2`` ``system`` ``0.12.1`` ``system`` ========== ========== .. _list_software_SPAdes_544: *SPAdes* ++++++++ Genome assembler for single-cell and isolates data sets *homepage*: http://bioinf.spbau.ru/en/spades ========== ============================================== version toolchain ========== ============================================== ``3.9.0`` ``foss/2016a``, ``foss/2016b`` ``3.10.1`` ``foss/2016b``, ``foss/2017a`` ``3.11.1`` ``foss/2017b``, ``foss/2018a`` ``3.12.0`` ``foss/2016b``, ``foss/2018a``, ``foss/2018b`` ``3.13.0`` ``foss/2018b`` ``3.13.1`` ``GCC/8.2.0-2.31.1`` ========== ============================================== .. _list_software_spaln_542: *spaln* +++++++ Spaln (space-efficient spliced alignment) is a stand-alone program that maps and aligns a set of cDNA or protein sequences onto a whole genomic sequence in a single job. *homepage*: https://github.com/ogotoh/spaln ========== ======================================== version toolchain ========== ======================================== ``2.3.3c`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ========== ======================================== .. _list_software_Spark_513: *Spark* +++++++ Spark is Hadoop MapReduce done in memory *homepage*: https://spark.apache.org ========= =========================================== =============================== version versionsuffix toolchain ========= =========================================== =============================== ``1.3.0`` ``system`` ``1.4.1`` ``system`` ``1.5.0`` ``system`` ``1.6.0`` ``system`` ``1.6.1`` ``system`` ``2.0.0`` ``system`` ``2.0.2`` ``system`` ``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_144`` ``system`` ``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_152`` ``system`` ``2.2.0`` ``-Hadoop-2.6-Java-1.8.0_152-Python-3.6.3`` ``intel/2017b`` ``2.3.0`` ``-Hadoop-2.7-Java-1.8.0_162`` ``system`` ``2.4.0`` ``-Hadoop-2.7-Java-1.8`` ``system`` ``2.4.0`` ``-Hadoop-2.7-Java-1.8-Python-3.6.6`` ``intel/2018b`` ``2.4.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.4.0`` ``-Python-3.6.6`` ``intel/2018b`` ========= =========================================== =============================== .. _list_software_sparsehash_1074: *sparsehash* ++++++++++++ An extremely memory-efficient hash_map implementation. 2 bits/entry overhead! The SparseHash library contains several hash-map implementations, including implementations that optimize for space or speed. *homepage*: https://github.com/sparsehash/sparsehash ========= =========================================================================================================== version toolchain ========= =========================================================================================================== ``2.0.2`` ``foss/2016a`` ``2.0.3`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``foss/2016b``, ``intel/2017a`` ========= =========================================================================================================== .. _list_software_spectral.methods_1664: *spectral.methods* ++++++++++++++++++ Contains some implementations of Singular Spectrum Analysis (SSA) for the gapfilling and spectral decomposition of time series. *homepage*: https://cran.r-project.org/web/packages/spectral.methods ============= ============= =============== version versionsuffix toolchain ============= ============= =============== ``0.7.2.133`` ``-R-3.4.3`` ``intel/2017b`` ``0.7.2.133`` ``-R-3.4.4`` ``intel/2018a`` ============= ============= =============== .. _list_software_spglib_641: *spglib* ++++++++ Spglib is a library for finding and handling crystal symmetries written in C. *homepage*: https://atztogo.github.io/spglib/ ========= ========================= version toolchain ========= ========================= ``1.9.2`` ``intel/2016.02-GCC-4.9`` ``1.9.9`` ``intel/2017b`` ========= ========================= .. _list_software_spglib-python_1360: *spglib-python* +++++++++++++++ Spglib for Python. Spglib is a library for finding and handling crystal symmetries written in C. *homepage*: https://pypi.python.org/pypi/spglib ================ ================== =============== version versionsuffix toolchain ================ ================== =============== ``1.9.4.2`` ``-Python-2.7.12`` ``intel/2016b`` ``1.9.5`` ``-Python-2.7.12`` ``intel/2016b`` ``1.9.9.38`` ``-Python-2.7.13`` ``intel/2017a`` ``1.10.0.2`` ``-Python-2.7.14`` ``intel/2017b`` ``1.10.0.2`` ``-Python-3.6.3`` ``intel/2017b`` ``1.14.1.post0`` ``-Python-3.7.2`` ``intel/2019a`` ================ ================== =============== .. _list_software_Sphinx_634: *Sphinx* ++++++++ Sphinx is a tool that makes it easy to create intelligent and beautiful documentation. It was originally created for the new Python documentation, and it has excellent facilities for the documentation of Python projects, but C/C++ is already supported as well, and it is planned to add special support for other languages as well. *homepage*: http://sphinx.pocoo.org/ ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``1.4.8`` ``-Python-2.7.11`` ``foss/2016a`` ``1.4.8`` ``-Python-3.5.1`` ``foss/2016a`` ``1.8.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``1.8.1`` ``-Python-2.7.15`` ``foss/2018b`` ``1.8.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.8.1`` ``-Python-3.6.4`` ``foss/2018a`` ``1.8.1`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``1.8.3`` ``-Python-3.6.4`` ``intel/2018a`` ========= ================== =============================== .. _list_software_SpiceyPy_822: *SpiceyPy* ++++++++++ SpiceyPy is a Python wrapper for the NAIF C SPICE Toolkit (N65) *homepage*: https://github.com/AndrewAnnex/SpiceyPy ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``1.1.0`` ``-Python-2.7.12`` ``intel/2016b`` ``1.1.1`` ``-Python-3.6.1`` ``intel/2017a`` ``2.1.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``2.1.0`` ``-Python-3.6.4`` ``foss/2018a`` ========= ================== =============================== .. _list_software_SpiecEasi_886: *SpiecEasi* +++++++++++ Sparse InversE Covariance estimation for Ecological Association and Statistical Inference *homepage*: https://github.com/zdk123/SpiecEasi ============ ============= =============== version versionsuffix toolchain ============ ============= =============== ``1.0.0`` ``-R-3.4.4`` ``intel/2018a`` ``20160830`` ``-R-3.3.1`` ``intel/2016b`` ============ ============= =============== .. _list_software_SPLASH_459: *SPLASH* ++++++++ SPLASH is a free and open source visualisation tool for Smoothed Particle Hydrodynamics (SPH) simulations. *homepage*: http://users.monash.edu.au/~dprice/splash/index.html ========= ============== version toolchain ========= ============== ``2.8.0`` ``foss/2018b`` ========= ============== .. _list_software_SpliceMap_894: *SpliceMap* +++++++++++ SpliceMap is a de novo splice junction discovery and alignment tool. It offers high sensitivity and support for arbitrary RNA-seq read lengths. *homepage*: https://web.stanford.edu/group/wonglab/SpliceMap/ =========== ================== version toolchain =========== ================== ``3.3.5.2`` ``GCC/7.3.0-2.30`` =========== ================== .. _list_software_splitRef_841: *splitRef* ++++++++++ splitRef splits a reference haplotype file into smaller files with subsets of markers. The current version is a pre-release. *homepage*: http://www.sph.umich.edu/csg/yli/splitRef/index.html ========= ========== version toolchain ========= ========== ``0.0.2`` ``system`` ========= ========== .. _list_software_SPRNG_394: *SPRNG* +++++++ Scalable Parallel Pseudo Random Number Generators Library *homepage*: http://www.sprng.org/ ======== ============== version toolchain ======== ============== ``2.0b`` ``foss/2016a`` ======== ============== .. _list_software_Spyder_631: *Spyder* ++++++++ Spyder is an interactive Python development environment providing MATLAB-like features in a simple and light-weighted software. *homepage*: https://github.com/spyder-ide/spyder ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``3.1.4`` ``-Python-2.7.13`` ``intel/2017a`` ``3.3.1`` ``-Python-3.6.4`` ``foss/2018a`` ``3.3.2`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================== =============== .. _list_software_SQLite_562: *SQLite* ++++++++ SQLite: SQL Database Engine in a C Library *homepage*: http://www.sqlite.org/ ============ ==================================================================================================================================================================== version toolchain ============ ==================================================================================================================================================================== ``3.8.8.1`` ``GCC/4.8.4``, ``GCC/4.9.2`` ``3.8.10.2`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``gimkl/2.11.5`` ``3.9.2`` ``GCC/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``3.13.0`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016b`` ``3.14.1`` ``GCCcore/4.9.3`` ``3.17.0`` ``GCCcore/6.3.0`` ``3.20.1`` ``GCCcore/6.4.0`` ``3.21.0`` ``GCCcore/6.4.0`` ``3.23.0`` ``GCCcore/6.4.0`` ``3.24.0`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``3.26.0`` ``GCCcore/8.2.0`` ``3.27.2`` ``GCCcore/8.2.0`` ``3.29.0`` ``GCCcore/8.3.0`` ============ ==================================================================================================================================================================== .. _list_software_SqueezeMeta_1129: *SqueezeMeta* +++++++++++++ SqueezeMeta is a full automatic pipeline for metagenomics/metatranscriptomics, covering all steps of the analysis. *homepage*: https://github.com/jtamames/SqueezeMeta ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``0.4.3`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== ============== .. _list_software_SRA-Toolkit_1017: *SRA-Toolkit* +++++++++++++ The SRA Toolkit, and the source-code SRA System Development Kit (SDK), will allow you to programmatically access data housed within SRA and convert it from the SRA format *homepage*: http://www.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=software =========== =================== ========== version versionsuffix toolchain =========== =================== ========== ``2.3.5`` ``-centos_linux64`` ``system`` ``2.5.4-1`` ``-centos_linux64`` ``system`` ``2.5.7`` ``-centos_linux64`` ``system`` ``2.8.2-1`` ``-centos_linux64`` ``system`` ``2.9.0`` ``-centos_linux64`` ``system`` ``2.9.2`` ``-ubuntu64`` ``system`` ``2.9.4`` ``-centos_linux64`` ``system`` ``2.9.6-1`` ``-centos_linux64`` ``system`` =========== =================== ========== .. _list_software_SRPRISM_560: *SRPRISM* +++++++++ Single Read Paired Read Indel Substitution Minimizer *homepage*: https://github.com/ncbi/SRPRISM ========= ============= ================= version versionsuffix toolchain ========= ============= ================= ``3.0.0`` ``foss/2018b`` ``3.1.1`` ``-Java-11`` ``GCCcore/8.2.0`` ========= ============= ================= .. _list_software_SSAHA2_418: *SSAHA2* ++++++++ SSAHA2 (Sequence Search and Alignment by Hashing Algorithm) is a pairwise sequence alignment program designed for the efficient mapping of sequencing reads onto genomic reference sequences. SSAHA2 reads of most sequencing platforms (ABI-Sanger, Roche 454, Illumina-Solexa) and a range of output formats (SAM, CIGAR, PSL etc.) are supported. A pile-up pipeline for analysis and genotype calling is available as a separate package. *homepage*: http://www.sanger.ac.uk/resources/software/ssaha2/ ========= ============= ========== version versionsuffix toolchain ========= ============= ========== ``2.5.5`` ``-i686`` ``system`` ``2.5.5`` ``-x86_64`` ``system`` ========= ============= ========== .. _list_software_SSPACE_Basic_1024: *SSPACE_Basic* ++++++++++++++ SSPACE Basic, SSAKE-based Scaffolding of Pre-Assembled Contigs after Extension *homepage*: https://github.com/nsoranzo/sspace_basic ========= ================ =============== version versionsuffix toolchain ========= ================ =============== ``2.1.1`` ``-Perl-5.24.1`` ``intel/2017a`` ``2.1.1`` ``-Perl-5.26.0`` ``intel/2017b`` ========= ================ =============== .. _list_software_Stacks_617: *Stacks* ++++++++ Stacks is a software pipeline for building loci from short-read sequences, such as those generated on the Illumina platform. Stacks was developed to work with restriction enzyme-based data, such as RAD-seq, for the purpose of building genetic maps and conducting population genomics and phylogeography. *homepage*: http://catchenlab.life.illinois.edu/stacks ============== ============================================================================== version toolchain ============== ============================================================================== ``1.40`` ``foss/2016a`` ``1.42`` ``foss/2016a`` ``1.44`` ``foss/2016a`` ``1.45`` ``foss/2016a`` ``1.46`` ``intel/2017a`` ``1.47`` ``foss/2016a`` ``1.48`` ``intel/2017b``, ``intel/2018b`` ``2.0`` ``foss/2018a``, ``intel/2018a`` ``2.0Beta7c`` ``intel/2017b`` ``2.0Beta8c`` ``intel/2017b`` ``2.0Beta9`` ``intel/2018a`` ``2.0Beta10a`` ``foss/2018a`` ``2.2`` ``foss/2018a`` ``2.3b`` ``foss/2018a`` ``2.3e`` ``foss/2018b`` ``2.41`` ``GCC/8.2.0-2.31.1``, ``foss/2018b``, ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ============== ============================================================================== .. _list_software_STAMP_389: *STAMP* +++++++ STAMP is a tool for characterizing similarities between transcription factor binding motifs *homepage*: http://www.benoslab.pitt.edu/stamp/ ======= ================================ version toolchain ======= ================================ ``1.2`` ``intel/2016a`` ``1.3`` ``intel/2016a``, ``intel/2016b`` ======= ================================ .. _list_software_StaMPS_536: *StaMPS* ++++++++ A software package to extract ground displacements from time series of synthetic aperture radar (SAR) acquisitions. *homepage*: http://homepages.see.leeds.ac.uk/~earahoo/stamps/ ========= ================ =============== version versionsuffix toolchain ========= ================ =============== ``3.3b1`` ``-Perl-5.24.1`` ``intel/2017a`` ========= ================ =============== .. _list_software_Stampy_638: *Stampy* ++++++++ Stampy is a package for the mapping of short reads from illumina sequencing machines onto a reference genome. *homepage*: http://www.well.ox.ac.uk/stampy ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``1.0.31`` ``-Python-2.7.12`` ``intel/2016b`` ``1.0.32`` ``-Python-2.7.14`` ``intel/2018a`` ========== ================== =============== .. _list_software_STAR_314: *STAR* ++++++ STAR aligns RNA-seq reads to a reference genome using uncompressed suffix arrays. *homepage*: https://github.com/alexdobin/STAR ========== =============================================== version toolchain ========== =============================================== ``2.4.2a`` ``foss/2018b`` ``2.5.0a`` ``GNU/4.9.3-2.25`` ``2.5.2a`` ``foss/2016a`` ``2.5.2b`` ``intel/2016b`` ``2.5.3a`` ``intel/2017a``, ``intel/2017b`` ``2.5.4b`` ``foss/2016b``, ``foss/2017b``, ``intel/2017b`` ``2.6.0c`` ``foss/2018a``, ``intel/2018a`` ``2.6.1c`` ``foss/2018b`` ``2.7.0d`` ``foss/2018b`` ``2.7.0f`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` ``2.7.1a`` ``GCC/8.2.0-2.31.1``, ``foss/2018b`` ========== =============================================== .. _list_software_STAR-Fusion_987: *STAR-Fusion* +++++++++++++ STAR-Fusion uses the STAR aligner to identify candidate fusion transcripts supported by Illumina reads. STAR-Fusion further processes the output generated by the STAR aligner to map junction reads and spanning reads to a reference annotation set. *homepage*: https://github.com/STAR-Fusion/STAR-Fusion ========= ============================= ==================== version versionsuffix toolchain ========= ============================= ==================== ``1.5.0`` ``-Perl-5.28.0`` ``foss/2018b`` ``1.6.0`` ``-Perl-5.28.1-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` ========= ============================= ==================== .. _list_software_Stata_509: *Stata* +++++++ Stata is a complete, integrated statistical software package that provides everything you need for data analysis, data management, and graphics. *homepage*: https://www.stata.com/ ======= ========== version toolchain ======= ========== ``15`` ``system`` ======= ========== .. _list_software_statsmodels_1203: *statsmodels* +++++++++++++ Statsmodels is a Python module that provides classes and functions for the estimation of many different statistical models, as well as for conducting statistical tests, and statistical data exploration. *homepage*: https://www.statsmodels.org ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``0.6.1`` ``-Python-2.7.13`` ``foss/2017a`` ``0.6.1`` ``-Python-3.5.1`` ``intel/2016a`` ``0.6.1`` ``-Python-3.5.2`` ``intel/2016b`` ``0.8.0`` ``-Python-2.7.13`` ``intel/2017a`` ``0.9.0`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``0.10.1`` ``foss/2019a`` ========== ================== =============================== .. _list_software_STIR_322: *STIR* ++++++ Software for Tomographic Image Reconstruction *homepage*: http://stir.sourceforge.net/ ======= =============== version toolchain ======= =============== ``3.0`` ``intel/2018a`` ======= =============== .. _list_software_STREAM_460: *STREAM* ++++++++ The STREAM benchmark is a simple synthetic benchmark program that measures sustainable memory bandwidth (in MB/s) and the corresponding computation rate for simple vector kernels. *homepage*: https://www.cs.virginia.edu/stream/ ======== ========================================================================== version toolchain ======== ========================================================================== ``5.10`` ``GCC/7.3.0-2.30``, ``GCC/8.2.0-2.31.1``, ``intel/2016b``, ``intel/2018b`` ======== ========================================================================== .. _list_software_strelka_758: *strelka* +++++++++ Strelka2 is a fast and accurate small variant caller optimized for analysis of germline variation in small cohorts and somatic variation in tumor/normal sample pairs. *homepage*: https://github.com/Illumina/strelka ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``2.9.7`` ``intel/2018a`` ``2.9.9`` ``foss/2018b`` ``2.9.10`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ========== ================== =============================== .. _list_software_StringTie_921: *StringTie* +++++++++++ StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts. *homepage*: http://ccb.jhu.edu/software/%(namelower)/ ========== ================================== version toolchain ========== ================================== ``1.3.0`` ``intel/2016b`` ``1.3.3`` ``GCCcore/6.4.0``, ``intel/2017a`` ``1.3.3b`` ``foss/2016b`` ``1.3.5`` ``GCCcore/8.2.0``, ``foss/2018b`` ``2.0.3`` ``GCCcore/7.3.0`` ========== ================================== .. _list_software_Structure_977: *Structure* +++++++++++ The program structure is a free software package for using multi-locus genotype data to investigate population structure. *homepage*: https://web.stanford.edu/group/pritchardlab/structure.html ========= ====================================== version toolchain ========= ====================================== ``2.3.4`` ``iccifort/2019.3.199-GCC-8.3.0-2.32`` ========= ====================================== .. _list_software_Subread_710: *Subread* +++++++++ High performance read alignment, quantification and mutation discovery *homepage*: http://subread.sourceforge.net/ ============ ============================== version toolchain ============ ============================== ``1.5.0-p1`` ``foss/2016a``, ``foss/2016b`` ``1.6.3`` ``foss/2018b`` ``1.6.4`` ``foss/2018b`` ``2.0.0`` ``GCC/7.3.0-2.30`` ============ ============================== .. _list_software_Subversion_1072: *Subversion* ++++++++++++ Subversion is an open source version control system. *homepage*: http://subversion.apache.org/ ========== =============================== version toolchain ========== =============================== ``1.9.7`` ``iomkl/2018a`` ``1.9.9`` ``GCCcore/7.3.0`` ``1.10.0`` ``foss/2017b``, ``intel/2017b`` ``1.12.0`` ``GCCcore/8.2.0`` ========== =============================== .. _list_software_suds_447: *suds* ++++++ Lightweight SOAP client *homepage*: https://pypi.python.org/pypi/suds-py3 =========== ================= =============== version versionsuffix toolchain =========== ================= =============== ``1.3.3.0`` ``-Python-3.6.4`` ``intel/2018a`` =========== ================= =============== .. _list_software_SuiteSparse_1144: *SuiteSparse* +++++++++++++ SuiteSparse is a collection of libraries manipulate sparse matrices. *homepage*: https://faculty.cse.tamu.edu/davis/suitesparse.html ========= =================== ================================================================================================= version versionsuffix toolchain ========= =================== ================================================================================================= ``4.5.1`` ``-METIS-5.1.0`` ``foss/2016a``, ``intel/2016a`` ``4.5.2`` ``-METIS-5.1.0`` ``foss/2016a``, ``intel/2016a`` ``4.5.3`` ``-METIS-5.1.0`` ``foss/2016a``, ``foss/2016b``, ``intel/2016b`` ``4.5.3`` ``-ParMETIS-4.0.3`` ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``4.5.5`` ``-METIS-5.1.0`` ``foss/2017a``, ``intel/2017a`` ``4.5.5`` ``-ParMETIS-4.0.3`` ``foss/2017a``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``4.5.6`` ``-METIS-5.1.0`` ``foss/2017b`` ``5.1.2`` ``-METIS-5.1.0`` ``foss/2017b``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b`` ``5.1.2`` ``-ParMETIS-4.0.3`` ``foss/2017b``, ``intel/2017b`` ``5.4.0`` ``-METIS-5.1.0`` ``foss/2019a``, ``intel/2018b``, ``intel/2019a`` ``5.6.0`` ``-METIS-5.1.0`` ``foss/2019b`` ========= =================== ================================================================================================= .. _list_software_SUMACLUST_705: *SUMACLUST* +++++++++++ SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. *homepage*: http://metabarcoding.org/sumatra ========== ============== version toolchain ========== ============== ``1.0.20`` ``foss/2016a`` ========== ============== .. _list_software_SUMATRA_541: *SUMATRA* +++++++++ SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences. *homepage*: http://metabarcoding.org/sumatra ========== ============== version toolchain ========== ============== ``1.0.20`` ``foss/2016a`` ========== ============== .. _list_software_SUNDIALS_611: *SUNDIALS* ++++++++++ SUNDIALS: SUite of Nonlinear and DIfferential/ALgebraic Equation Solvers *homepage*: https://computation.llnl.gov/projects/sundials ========= ================================================================================================================== version toolchain ========= ================================================================================================================== ``2.6.2`` ``intel/2016b``, ``intel/2018b`` ``2.7.0`` ``foss/2016b``, ``foss/2017b``, ``foss/2018a``, ``intel/2016b``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``5.1.0`` ``intel/2019b`` ========= ================================================================================================================== .. _list_software_SuperLU_688: *SuperLU* +++++++++ SuperLU is a general purpose library for the direct solution of large, sparse, nonsymmetric systems of linear equations on high performance machines. *homepage*: http://crd-legacy.lbl.gov/~xiaoye/SuperLU/ ========= =============================== version toolchain ========= =============================== ``5.1.1`` ``foss/2016a``, ``intel/2016a`` ``5.2.1`` ``foss/2017b``, ``intel/2017b`` ========= =============================== .. _list_software_supermagic_1072: *supermagic* ++++++++++++ Very simple MPI sanity code. Nothing more, nothing less. *homepage*: https://github.com/hpc/supermagic ============ ============== version toolchain ============ ============== ``20170824`` ``foss/2017a`` ============ ============== .. _list_software_supernova_995: *supernova* +++++++++++ Supernova is a software package for de novo assembly from Chromium Linked-Reads that are made from a single whole-genome library from an individual DNA source *homepage*: https://support.10xgenomics.com/de-novo-assembly/software/overview/latest/welcome ========= ========== version toolchain ========= ========== ``2.0.1`` ``system`` ``2.1.1`` ``system`` ========= ========== .. _list_software_SVDetect_770: *SVDetect* ++++++++++ SVDetect is a application for the isolation and the type prediction of intra- and inter-chromosomal rearrangements from paired-end/mate-pair sequencing data provided by the high-throughput sequencing technologies. This tool aims to identifying structural variations with both clustering and sliding-window strategies, and helping in their visualization at the genome scale. *homepage*: http://svdetect.sourceforge.net/Site/Home.html ======== ================ ========================================================== version versionsuffix toolchain ======== ================ ========================================================== ``0.8b`` ``-Perl-5.26.0`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ======== ================ ========================================================== .. _list_software_SVDquest_799: *SVDquest* ++++++++++ SVDquartets-based species trees *homepage*: https://github.com/pranjalv123/SVDquest ============ =============== version toolchain ============ =============== ``20190627`` ``gompi/2019a`` ============ =============== .. _list_software_swarm_554: *swarm* +++++++ A robust and fast clustering method for amplicon-based studies *homepage*: https://github.com/torognes/swarm ========= ============== version toolchain ========= ============== ``2.2.2`` ``foss/2018b`` ========= ============== .. _list_software_SWASH_390: *SWASH* +++++++ SWASH is a general-purpose numerical tool for simulating unsteady, non-hydrostatic, free-surface, rotational flow and transport phenomena in coastal waters as driven by waves, tides, buoyancy and wind forces. *homepage*: http://swash.sourceforge.net/ ======== ============= ================================ version versionsuffix toolchain ======== ============= ================================ ``3.14`` ``-mpi`` ``intel/2016b``, ``intel/2017a`` ``4.01`` ``-mpi`` ``intel/2017a`` ======== ============= ================================ .. _list_software_SWIG_314: *SWIG* ++++++ SWIG is a software development tool that connects programs written in C and C++ with a variety of high-level programming languages. *homepage*: http://www.swig.org/ ========== ============================ ================================================================ version versionsuffix toolchain ========== ============================ ================================================================ ``3.0.8`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``3.0.8`` ``-Python-3.5.1`` ``foss/2016a`` ``3.0.10`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``3.0.10`` ``-Python-2.7.12-PCRE-8.39`` ``intel/2016b`` ``3.0.11`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``3.0.12`` ``GCCcore/8.2.0`` ``3.0.12`` ``-Python-2.7.13`` ``intel/2017a`` ``3.0.12`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``3.0.12`` ``-Python-2.7.15`` ``GCCcore/8.2.0``, ``foss/2018b``, ``intel/2018b`` ``3.0.12`` ``-Python-3.6.1`` ``intel/2017a`` ``3.0.12`` ``-Python-3.6.2`` ``foss/2017b``, ``intel/2018.00`` ``3.0.12`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b``, ``intel/2018.01`` ``3.0.12`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018a`` ``3.0.12`` ``-Python-3.6.6`` ``foss/2018b``, ``intel/2018b`` ``3.0.12`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ``4.0.1`` ``GCCcore/8.3.0`` ========== ============================ ================================================================ .. _list_software_SymEngine_911: *SymEngine* +++++++++++ SymEngine is a standalone fast C++ symbolic manipulation library. *homepage*: https://github.com/symengine/symengine ========= ============= ==================== version versionsuffix toolchain ========= ============= ==================== ``0.3.0`` ``-20181006`` ``intel/2018a`` ``0.4.0`` ``GCC/8.2.0-2.31.1`` ========= ============= ==================== .. _list_software_sympy_578: *sympy* +++++++ SymPy is a Python library for symbolic mathematics. It aims to become a full-featured computer algebra system (CAS) while keeping the code as simple as possible in order to be comprehensible and easily extensible. SymPy is written entirely in Python and does not require any external libraries. *homepage*: http://sympy.org/ ======= ================== =============================== version versionsuffix toolchain ======= ================== =============================== ``1.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``1.3`` ``-Python-2.7.14`` ``intel/2018a`` ``1.3`` ``-Python-2.7.15`` ``foss/2018b`` ``1.3`` ``-Python-3.6.4`` ``intel/2018a`` ``1.3`` ``-Python-3.6.6`` ``foss/2018b`` ``1.4`` ``foss/2019a``, ``intel/2019a`` ======= ================== =============================== .. _list_software_Szip_422: *Szip* ++++++ Szip compression software, providing lossless compression of scientific data *homepage*: https://www.hdfgroup.org/doc_resource/SZIP/ ========= ========================================================================================================================================================================================================================================================================= version toolchain ========= ========================================================================================================================================================================================================================================================================= ``2.1`` ``GCC/4.8.1``, ``GCCcore/5.4.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``intel/2017a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``2.1.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ========================================================================================================================================================================================================================================================================= .. _list_software_letter_t: *T* --- :ref:`list_software_tabix_536` - :ref:`list_software_taco_423` - :ref:`list_software_TagLib_563` - :ref:`list_software_TAMkin_548` - :ref:`list_software_taxator-tk_1039` - :ref:`list_software_tbb_312` - :ref:`list_software_tbl2asn_694` - :ref:`list_software_TCC_218` - :ref:`list_software_Tcl_291` - :ref:`list_software_tcsh_434` - :ref:`list_software_tecplot360ex_1137` - :ref:`list_software_TensorFlow_1043` - :ref:`list_software_TensorRT_801` - :ref:`list_software_Tesla-Deployment-Kit_1948` - :ref:`list_software_tesseract_974` - :ref:`list_software_testpath_877` - :ref:`list_software_TetGen_583` - :ref:`list_software_TEToolkit_895` - :ref:`list_software_texinfo_765` - :ref:`list_software_Text-CSV_702` - :ref:`list_software_Theano_607` - :ref:`list_software_THetA_438` - :ref:`list_software_thurstonianIRT_1454` - :ref:`list_software_TiCCutils_884` - :ref:`list_software_Tika_393` - :ref:`list_software_TiMBL_408` - :ref:`list_software_time_431` - :ref:`list_software_TINKER_461` - :ref:`list_software_TinyDB_554` - :ref:`list_software_Tk_191` - :ref:`list_software_Tkinter_737` - :ref:`list_software_TM-align_729` - :ref:`list_software_tmux_462` - :ref:`list_software_ToFu_382` - :ref:`list_software_TopHat_592` - :ref:`list_software_torchvision_1208` - :ref:`list_software_TotalView_927` - :ref:`list_software_tqdm_438` - :ref:`list_software_Tracer_609` - :ref:`list_software_TransDecoder_1214` - :ref:`list_software_Transrate_948` - :ref:`list_software_travis_665` - :ref:`list_software_TreeMix_702` - :ref:`list_software_TreeShrink_1023` - :ref:`list_software_TRF_236` - :ref:`list_software_Triangle_822` - :ref:`list_software_Trilinos_852` - :ref:`list_software_Trim_Galore_1109` - :ref:`list_software_trimAl_617` - :ref:`list_software_Trimmomatic_1158` - :ref:`list_software_Trinity_755` - :ref:`list_software_TRIQS_403` - :ref:`list_software_TRIQS-cthyb_986` - :ref:`list_software_TRIQS-dft_tools_1422` - :ref:`list_software_TRIQS-tprf_892` - :ref:`list_software_TRUST_418` - :ref:`list_software_TurboVNC_755` - :ref:`list_software_TVB_236` - :ref:`list_software_tvb-data_787` - :ref:`list_software_TVB-deps_709` - :ref:`list_software_tvb-framework_1351` - :ref:`list_software_tvb-library_1134` .. _list_software_tabix_536: *tabix* +++++++ Generic indexer for TAB-delimited genome position files *homepage*: http://samtools.sourceforge.net ========= ========================================================================================================= version toolchain ========= ========================================================================================================= ``0.2.6`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2016a``, ``intel/2016a``, ``intel/2016b`` ========= ========================================================================================================= .. _list_software_taco_423: *taco* ++++++ Multi-sample transcriptome assembly from RNA-Seq *homepage*: http://tacorna.github.io ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.5.1`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== .. _list_software_TagLib_563: *TagLib* ++++++++ TagLib is a library for reading and editing the meta-data of several popular audio formats. *homepage*: https://taglib.org/ ========== ================= version toolchain ========== ================= ``1.11.1`` ``GCCcore/8.2.0`` ========== ================= .. _list_software_TAMkin_548: *TAMkin* ++++++++ TAMkin is a post-processing toolkit for normal mode analysis, thermochemistry and reaction kinetics. It uses a Hessian computation from a standard computational chemistry program as its input. *homepage*: https://molmod.github.io/tamkin/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.0.9`` ``-Python-2.7.11`` ``intel/2016a`` ``1.2.4`` ``-Python-2.7.14`` ``intel/2017b`` ``1.2.6`` ``-Python-3.7.2`` ``intel/2019a`` ========= ================== =============== .. _list_software_taxator-tk_1039: *taxator-tk* ++++++++++++ A set of programs for the taxonomic analysis of nucleotide sequence data *homepage*: https://github.com/fungs/taxator-tk ========= =============================== version toolchain ========= =============================== ``1.3.3`` ``foss/2018b``, ``gompi/2019a`` ========= =============================== .. _list_software_tbb_312: *tbb* +++++ Intel Threading Building Blocks (Intel TBB) is a widely used, award-winning C++ template library for creating reliable, portable, and scalable parallel applications. Use Intel TBB for a simple and rapid way of developing robust task-based parallel applications that scale to available processor cores, are compatible with multiple environments, and are easier to maintain. Intel TBB is the most proficient way to implement future-proof parallel applications that tap into the power and performance of multicore and manycore hardware platforms. *homepage*: https://software.intel.com/en-us/articles/intel-tbb/ ============== ================================================== version toolchain ============== ================================================== ``4.0.0.233`` ``system`` ``4.0.5.339`` ``system`` ``4.3.6.211`` ``system`` ``4.4.2.152`` ``system`` ``2017.2.132`` ``system`` ``2017.4.174`` ``system`` ``2017.6.196`` ``system`` ``2017_U5`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2017a`` ``2017_U6`` ``GCCcore/6.3.0``, ``intel/2017a`` ``2018_U1`` ``GCCcore/6.4.0`` ``2018_U2`` ``GCCcore/6.4.0`` ``2018_U3`` ``GCCcore/6.4.0`` ``2018_U5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2019_U4`` ``GCCcore/8.2.0`` ``2019_U9`` ``GCCcore/8.3.0`` ============== ================================================== .. _list_software_tbl2asn_694: *tbl2asn* +++++++++ Tbl2asn is a command-line program that automates the creation of sequence records for submission to GenBank *homepage*: https://www.ncbi.nlm.nih.gov/genbank/tbl2asn2/ ============ ============= ========== version versionsuffix toolchain ============ ============= ========== ``25.8`` ``-linux64`` ``system`` ``20180227`` ``-linux64`` ``system`` ============ ============= ========== .. _list_software_TCC_218: *TCC* +++++ The Tiny C Compiler (aka TCC, tCc, or TinyCC) is an x86 and x86-64 C compiler created by Fabrice Bellard. It is designed to work for slow computers with little disk space and can run shebang style !/usr/bin/tcc . TCC is distributed under the LGPL. TCC claims to implement all of ANSI C (C89/C90),[1] much of the new ISO C99 standard, and many GNU C extensions including inline assembly. *homepage*: http://bellard.org/tcc/ ========== ========== version toolchain ========== ========== ``0.9.26`` ``system`` ========== ========== .. _list_software_Tcl_291: *Tcl* +++++ Tcl (Tool Command Language) is a very powerful but easy to learn dynamic programming language, suitable for a very wide range of uses, including web and desktop applications, networking, administration, testing and many more. *homepage*: https://www.tcl.tk/ ========== ========================================================================================================================================================================= version toolchain ========== ========================================================================================================================================================================= ``8.5.19`` ``foss/2017a`` ``8.6.3`` ``GCC/4.8.4``, ``GCC/4.9.2`` ``8.6.4`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``8.6.5`` ``GCC/4.9.3-2.25``, ``GCC/5.4.0-2.26``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016b`` ``8.6.6`` ``GCCcore/4.9.3``, ``GCCcore/6.3.0`` ``8.6.7`` ``GCCcore/6.4.0`` ``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0`` ``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========== ========================================================================================================================================================================= .. _list_software_tcsh_434: *tcsh* ++++++ Tcsh is an enhanced, but completely compatible version of the Berkeley UNIX C shell (csh). It is a command language interpreter usable both as an interactive login shell and a shell script command processor. It includes a command-line editor, programmable word completion, spelling correction, a history mechanism, job control and a C-like syntax. *homepage*: https://www.tcsh.org =========== ======================================================= version toolchain =========== ======================================================= ``6.19.00`` ``intel/2016a`` ``6.20.00`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``6.22.02`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` =========== ======================================================= .. _list_software_tecplot360ex_1137: *tecplot360ex* ++++++++++++++ Quickly plot and animate your CFD results exactly the way you want. Analyze complex solutions, arrange multiple layouts, and communicate your results with professional images and animations. *homepage*: http://www.tecplot.com/products/tecplot-360/ =========== ========== version toolchain =========== ========== ``linux64`` ``system`` =========== ========== .. _list_software_TensorFlow_1043: *TensorFlow* ++++++++++++ An open-source software library for Machine Intelligence *homepage*: https://www.tensorflow.org/ ========== ============================= =================================================== version versionsuffix toolchain ========== ============================= =================================================== ``0.12.1`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``0.12.1`` ``-Python-3.5.2`` ``foss/2016b``, ``intel/2016b`` ``1.0.1`` ``-Python-2.7.12`` ``intel/2016b`` ``1.0.1`` ``-Python-3.5.2`` ``intel/2016b`` ``1.1.0`` ``-Python-2.7.13`` ``intel/2017a`` ``1.1.0`` ``-Python-3.6.1`` ``intel/2017a`` ``1.2.0`` ``-Python-3.6.1`` ``intel/2017a`` ``1.2.1`` ``-GPU-Python-3.5.2`` ``foss/2016b`` ``1.2.1`` ``-Python-3.5.2`` ``foss/2016b`` ``1.3.0`` ``-Python-2.7.13`` ``intel/2017a`` ``1.3.0`` ``-Python-3.6.1`` ``intel/2017a`` ``1.3.0`` ``-Python-3.6.3`` ``intel/2017b`` ``1.4.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.4.1`` ``-Python-3.6.3`` ``foss/2017b`` ``1.5.0`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.6.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.6.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` ``1.7.0`` ``-Python-3.6.4`` ``foss/2018a`` ``1.7.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` ``1.8.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b`` ``1.8.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b`` ``1.8.0`` ``-Python-3.6.4`` ``foss/2018a``, ``fosscuda/2018a``, ``intel/2018a`` ``1.10.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``1.10.1`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``1.10.1`` ``-Python-3.6.6`` ``foss/2018b`` ``1.11.0`` ``-Python-3.6.6`` ``foss/2018b`` ``1.12.0`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``1.12.0`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``1.13.1`` ``-Python-3.6.6`` ``foss/2018b`` ``1.13.1`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``1.14.0`` ``-Python-3.7.2`` ``foss/2019a``, ``fosscuda/2019a`` ``1.15.0`` ``-Python-3.7.4`` ``foss/2019b``, ``fosscuda/2019b`` ``2.0.0`` ``-Python-3.7.2`` ``foss/2019a`` ``2.0.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` ``2.1.0`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========== ============================= =================================================== .. _list_software_TensorRT_801: *TensorRT* ++++++++++ NVIDIA TensorRT is a platform for high-performance deep learning inference *homepage*: https://developer.nvidia.com/tensorrt =========== ================== ================== version versionsuffix toolchain =========== ================== ================== ``4.0.1.6`` ``-Python-2.7.15`` ``fosscuda/2018b`` =========== ================== ================== .. _list_software_Tesla-Deployment-Kit_1948: *Tesla-Deployment-Kit* ++++++++++++++++++++++ The Tesla Deployment Kit is a set of tools provided primarily for the NVIDIA Tesla range of GPUs. They aim to empower users to better manage their NVIDIA GPUs by providing a broad range of functionalities. The kit contains: * NVIDIA Management Library (NVML), * Tesla Deployment Kit - Linux Edition (Aug 1st, 2013) *homepage*: https://developer.nvidia.com/tesla-deployment-kit ============ ========== version toolchain ============ ========== ``5.319.43`` ``system`` ============ ========== .. _list_software_tesseract_974: *tesseract* +++++++++++ Tesseract is an optical character recognition engine *homepage*: https://github.com/tesseract-ocr/tesseract ========= ================= version toolchain ========= ================= ``4.0.0`` ``GCCcore/7.3.0`` ``4.1.0`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_testpath_877: *testpath* ++++++++++ Test utilities for code working with files and commands *homepage*: https://github.com/jupyter/testpath ======= ================== =============================== version versionsuffix toolchain ======= ================== =============================== ``0.3`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``0.3`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``0.3`` ``-Python-3.5.1`` ``foss/2016a`` ``0.3`` ``-Python-3.5.2`` ``intel/2016b`` ======= ================== =============================== .. _list_software_TetGen_583: *TetGen* ++++++++ A Quality Tetrahedral Mesh Generator and a 3D Delaunay Triangulator *homepage*: http://wias-berlin.de/software/index.jsp?id=TetGen ========= ================= version toolchain ========= ================= ``1.5.0`` ``GCCcore/6.4.0`` ========= ================= .. _list_software_TEToolkit_895: *TEToolkit* +++++++++++ Tools for estimating differential enrichment of Transposable Elements and other highly repetitive regions *homepage*: http://hammelllab.labsites.cshl.edu/software/#TEToolkit ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``1.5.1`` ``-Python-2.7.11`` ``foss/2016a`` ========= ================== ============== .. _list_software_texinfo_765: *texinfo* +++++++++ Texinfo is the official documentation format of the GNU project. *homepage*: https://www.gnu.org/software/texinfo/ ========= ==================================== version toolchain ========= ==================================== ``4.13a`` ``system`` ``5.2`` ``GCC/4.8.2`` ``6.4`` ``GCCcore/5.4.0`` ``6.5`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``6.6`` ``GCCcore/8.2.0`` ``6.7`` ``GCCcore/8.3.0`` ========= ==================================== .. _list_software_Text-CSV_702: *Text-CSV* ++++++++++ Text-CSV parser *homepage*: https://metacpan.org/pod/Text::CSV ======== ================ ============== version versionsuffix toolchain ======== ================ ============== ``1.33`` ``-Perl-5.22.1`` ``foss/2016a`` ======== ================ ============== .. _list_software_Theano_607: *Theano* ++++++++ Theano is a Python library that allows you to define, optimize, and evaluate mathematical expressions involving multi-dimensional arrays efficiently. *homepage*: https://deeplearning.net/software/theano ========= ================== ======================================= version versionsuffix toolchain ========= ================== ======================================= ``0.8.2`` ``-Python-2.7.11`` ``foss/2016a`` ``0.8.2`` ``-Python-3.5.1`` ``foss/2016a`` ``0.8.2`` ``-Python-3.5.2`` ``intel/2016b`` ``0.9.0`` ``-Python-2.7.13`` ``intel/2017a`` ``0.9.0`` ``-Python-3.6.1`` ``intel/2017a`` ``1.0.0`` ``-Python-2.7.14`` ``intel/2017b`` ``1.0.0`` ``-Python-3.6.3`` ``intel/2017b`` ``1.0.1`` ``-Python-3.6.3`` ``foss/2017b``, ``intel/2017b`` ``1.0.2`` ``-Python-2.7.14`` ``fosscuda/2017b``, ``intelcuda/2017b`` ``1.0.2`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``1.0.2`` ``-Python-3.6.3`` ``fosscuda/2017b``, ``intelcuda/2017b`` ``1.0.2`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.0.3`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``1.0.4`` ``foss/2019a``, ``fosscuda/2019a`` ``1.0.4`` ``-Python-3.6.4`` ``foss/2018a`` ``1.0.4`` ``-Python-3.6.6`` ``fosscuda/2018b`` ========= ================== ======================================= .. _list_software_THetA_438: *THetA* +++++++ Tumor Heterogeneity Analysis (THetA) and THetA2 are algorithms that estimate the tumor purity and clonal/subclonal copy number aberrations directly from high-throughput DNA sequencing data. *homepage*: https://github.com/raphael-group/THetA ======= ================== ============== version versionsuffix toolchain ======= ================== ============== ``0.7`` ``-Python-2.7.15`` ``foss/2018b`` ======= ================== ============== .. _list_software_thurstonianIRT_1454: *thurstonianIRT* ++++++++++++++++ Fit Thurstonian IRT models in R using Stan, lavaan, or Mplus *homepage*: https://github.com/paul-buerkner/thurstonianIRT ========= ============= ============== version versionsuffix toolchain ========= ============= ============== ``0.9.0`` ``-R-3.6.0`` ``foss/2019a`` ========= ============= ============== .. _list_software_TiCCutils_884: *TiCCutils* +++++++++++ TiCC utils is a collection of generic C++ software which is used in a lot of programs produced at Tilburg centre for Cognition and Communication (TiCC) at Tilburg University and Centre for Dutch Language and Speech at University of Antwerp. *homepage*: https://github.com/LanguageMachines/ticcutils ======== ================================ version toolchain ======== ================================ ``0.11`` ``foss/2016a`` ``0.21`` ``iimpi/2019a``, ``intel/2018b`` ======== ================================ .. _list_software_Tika_393: *Tika* ++++++ The Apache Tika toolkit detects and extracts metadata and text from over a thousand different file types (such as PPT, XLS, and PDF). *homepage*: https://tika.apache.org/ ======== ========== version toolchain ======== ========== ``1.16`` ``system`` ======== ========== .. _list_software_TiMBL_408: *TiMBL* +++++++ TiMBL (Tilburg Memory Based Learner) is an open source software package implementing several memory-based learning algorithms, among which IB1-IG, an implementation of k-nearest neighbor classification with feature weighting suitable for symbolic feature spaces, and IGTree, a decision-tree approximation of IB1-IG. All implemented algorithms have in common that they store some representation of the training set explicitly in memory. During testing, new cases are classified by extrapolation from the most similar stored cases. *homepage*: http://ilk.uvt.nl/timbl/ ========== ================================ version toolchain ========== ================================ ``6.4.7`` ``foss/2016a`` ``6.4.13`` ``iimpi/2019a``, ``intel/2018b`` ========== ================================ .. _list_software_time_431: *time* ++++++ The `time' command runs another program, then displays information about the resources used by that program, collected by the system while the program was running. *homepage*: https://www.gnu.org/software/time/ ======= ================= version toolchain ======= ================= ``1.7`` ``system`` ``1.9`` ``GCCcore/8.3.0`` ======= ================= .. _list_software_TINKER_461: *TINKER* ++++++++ The TINKER molecular modeling software is a complete and general package for molecular mechanics and dynamics, with some special features for biopolymers. *homepage*: http://dasher.wustl.edu/tinker ========= ============== version toolchain ========= ============== ``8.6.1`` ``foss/2018b`` ========= ============== .. _list_software_TinyDB_554: *TinyDB* ++++++++ TinyDB is a lightweight document oriented database optimized for your happiness :) It's written in pure Python and has no external dependencies. The target are small apps that would be blown away by a SQL-DB or an external database server. *homepage*: https://tinydb.readthedocs.io/ ========== ================= version toolchain ========== ================= ``3.15.2`` ``GCCcore/8.3.0`` ========== ================= .. _list_software_Tk_191: *Tk* ++++ Tk is an open source, cross-platform widget toolchain that provides a library of basic elements for building a graphical user interface (GUI) in many different programming languages. *homepage*: https://www.tcl.tk/ ========= ================= ================================================================================================================================================ version versionsuffix toolchain ========= ================= ================================================================================================================================================ ``8.6.3`` ``-no-X11`` ``GCC/4.8.4``, ``GCC/4.9.2`` ``8.6.4`` ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25`` ``8.6.4`` ``-libX11-1.6.3`` ``intel/2016a`` ``8.6.4`` ``-no-X11`` ``GCC/4.9.3-2.25``, ``GNU/4.9.3-2.25``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a`` ``8.6.5`` ``GCC/5.4.0-2.26``, ``GCCcore/6.3.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``iccifort/2016.3.210-GCC-5.4.0-2.26``, ``intel/2016b`` ``8.6.6`` ``foss/2017a``, ``intel/2017a`` ``8.6.7`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``8.6.8`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``foss/2018a``, ``iomkl/2018a`` ``8.6.9`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ================= ================================================================================================================================================ .. _list_software_Tkinter_737: *Tkinter* +++++++++ Tkinter module, built with the Python buildsystem *homepage*: https://python.org/ ========== ================== ========================================================================================================= version versionsuffix toolchain ========== ================== ========================================================================================================= ``2.7.13`` ``-Python-2.7.13`` ``foss/2017a``, ``intel/2017a`` ``2.7.14`` ``-Python-2.7.14`` ``foss/2017b``, ``foss/2018a``, ``fosscuda/2017b``, ``intel/2017b``, ``intel/2018a``, ``intelcuda/2017b`` ``2.7.15`` ``GCCcore/8.2.0`` ``2.7.15`` ``-Python-2.7.15`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b`` ``3.6.1`` ``-Python-3.6.1`` ``foss/2017a``, ``intel/2017a`` ``3.6.2`` ``-Python-3.6.2`` ``foss/2017b`` ``3.6.3`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``3.6.4`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a``, ``iomkl/2018.02``, ``iomkl/2018a`` ``3.6.6`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018b``, ``iomkl/2018b`` ``3.7.2`` ``GCCcore/8.2.0`` ``3.7.4`` ``GCCcore/8.3.0`` ========== ================== ========================================================================================================= .. _list_software_TM-align_729: *TM-align* ++++++++++ This package unifies protein structure alignment and RNA structure alignment into the standard TM-align program for single chain structure alignment, MM-align program for multi-chain structure alignment, and TM-score program for sequence dependent structure superposition. *homepage*: https://zhanglab.ccmb.med.umich.edu/RNA-align/TMalign/ ============ =============================== version toolchain ============ =============================== ``20180426`` ``foss/2018b``, ``intel/2019a`` ============ =============================== .. _list_software_tmux_462: *tmux* ++++++ tmux is a terminal multiplexer. It lets you switch easily between several programs in one terminal, detach them (they keep running in the background) and reattach them to a different terminal. *homepage*: http://tmux.sourceforge.net/ ======== ============================== version toolchain ======== ============================== ``1.9a`` ``GCC/4.9.2`` ``2.2`` ``GCCcore/4.9.3`` ``2.3`` ``GCC/5.4.0-2.26``, ``system`` ======== ============================== .. _list_software_ToFu_382: *ToFu* ++++++ Tomography for Fusion. *homepage*: https://github.com/ToFuProject/tofu ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``1.3.17`` ``-Python-2.7.14`` ``foss/2018a`` ``1.3.17`` ``-Python-3.6.4`` ``foss/2018a`` ``1.4.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``1.4.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``1.4.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ========== ================== =============================== .. _list_software_TopHat_592: *TopHat* ++++++++ TopHat is a fast splice junction mapper for RNA-Seq reads. *homepage*: http://ccb.jhu.edu/software/tophat/ ========= ================== ================================================================================ version versionsuffix toolchain ========= ================== ================================================================================ ``2.1.0`` ``-Python-2.7.14`` ``intel/2018a`` ``2.1.1`` ``foss/2016a``, ``foss/2016b``, ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``2.1.2`` ``foss/2018b`` ========= ================== ================================================================================ .. _list_software_torchvision_1208: *torchvision* +++++++++++++ Datasets, Transforms and Models specific to Computer Vision *homepage*: https://github.com/pytorch/vision ========= ============================= ================================== version versionsuffix toolchain ========= ============================= ================================== ``0.2.0`` ``-Python-3.6.4`` ``intel/2018a`` ``0.2.0`` ``-Python-3.6.4-CUDA-9.1.85`` ``foss/2018a`` ``0.2.2`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``0.3.0`` ``-Python-3.7.2`` ``foss/2019a`` ``0.4.2`` ``-Python-3.7.4`` ``fosscuda/2019b`` ========= ============================= ================================== .. _list_software_TotalView_927: *TotalView* +++++++++++ TotalView is a GUI-based source code defect analysis tool that gives you unprecedented control over processes and thread execution and visibility into program state and variables. It allows you to debug one or many processes and/or threads in a single window with complete control over program execution. This allows you to set breakpoints, stepping line by line through the code on a single thread, or with coordinated groups of processes or threads, and run or halt arbitrary sets of processes or threads. You can reproduce and troubleshoot difficult problems that can occur in concurrent programs that take advantage of threads, OpenMP, MPI, GPUs or coprocessors. *homepage*: http://www.roguewave.com/products/totalview.aspx ============ ================= ========== version versionsuffix toolchain ============ ================= ========== ``8.11.0-0`` ``-linux-x86-64`` ``system`` ``8.11.0-2`` ``-linux-x86-64`` ``system`` ``8.12.0-0`` ``-linux-x86-64`` ``system`` ============ ================= ========== .. _list_software_tqdm_438: *tqdm* ++++++ A fast, extensible progress bar for Python and CLI *homepage*: https://github.com/tqdm/tqdm ========== ================== ================= version versionsuffix toolchain ========== ================== ================= ``4.24.0`` ``-Python-2.7.15`` ``foss/2018b`` ``4.24.0`` ``-Python-3.5.1`` ``foss/2016a`` ``4.29.0`` ``-Python-3.6.4`` ``intel/2018a`` ``4.32.1`` ``GCCcore/8.2.0`` ========== ================== ================= .. _list_software_Tracer_609: *Tracer* ++++++++ Tracer is a graphical tool for visualization and diagnostics of MCMC output. *homepage*: https://github.com/beast-dev/tracer ========= ================= version toolchain ========= ================= ``1.7.1`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_TransDecoder_1214: *TransDecoder* ++++++++++++++ TransDecoder identifies candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to the genome using Tophat and Cufflinks. *homepage*: https://github.com/TransDecoder/TransDecoder/wiki ========= ================ =============== version versionsuffix toolchain ========= ================ =============== ``2.1.0`` ``-Perl-5.24.1`` ``intel/2017a`` ========= ================ =============== .. _list_software_Transrate_948: *Transrate* +++++++++++ Transrate is software for de-novo transcriptome assembly quality analysis. It examines your assembly in detail and compares it to experimental evidence such as the sequencing reads, reporting quality scores for contigs and assemblies. This allows you to choose between assemblers and parameters, filter out the bad contigs from an assembly, and help decide when to stop trying to improve the assembly. *homepage*: http://hibberdlab.com/transrate/ ========= ========== version toolchain ========= ========== ``1.0.3`` ``system`` ========= ========== .. _list_software_travis_665: *travis* ++++++++ Travis CI Client (CLI and Ruby library) *homepage*: https://github.com/travis-ci/travis.rb ========= =============== ========== version versionsuffix toolchain ========= =============== ========== ``1.8.2`` ``-Ruby-2.3.1`` ``system`` ``1.8.4`` ``-Ruby-2.3.3`` ``system`` ========= =============== ========== .. _list_software_TreeMix_702: *TreeMix* +++++++++ TreeMix is a method for inferring the patterns of population splits and mixtures in the history of a set of populations. *homepage*: http://bitbucket.org/nygcresearch/treemix ======== =============== version toolchain ======== =============== ``1.13`` ``intel/2018a`` ======== =============== .. _list_software_TreeShrink_1023: *TreeShrink* ++++++++++++ TreeShrink is an algorithm for detecting abnormally long branches in one or more phylogenetic trees. *homepage*: https://github.com/uym2/TreeShrink ========= ================= ==================== version versionsuffix toolchain ========= ================= ==================== ``1.3.2`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` ========= ================= ==================== .. _list_software_TRF_236: *TRF* +++++ Tandem repeats finder: a program to analyze DNA sequences. Legacy version. *homepage*: https://tandem.bu.edu/trf/trf.html ======== ============= ========== version versionsuffix toolchain ======== ============= ========== ``4.09`` ``-linux64`` ``system`` ======== ============= ========== .. _list_software_Triangle_822: *Triangle* ++++++++++ Triangle generates exact Delaunay triangulations, constrained Delaunay triangulations, conforming Delaunay triangulations, Voronoi diagrams, and high-quality triangular meshes. The latter can be generated with no small or large angles, and are thus suitable for finite element analysis. *homepage*: http://www.cs.cmu.edu/~quake/triangle.html ======= ==================================================================================================== version toolchain ======= ==================================================================================================== ``1.6`` ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2018a``, ``intel/2016b``, ``intel/2017a``, ``intel/2018a`` ======= ==================================================================================================== .. _list_software_Trilinos_852: *Trilinos* ++++++++++ The Trilinos Project is an effort to develop algorithms and enabling technologies within an object-oriented software framework for the solution of large-scale, complex multi-physics engineering and scientific problems. A unique design feature of Trilinos is its focus on packages. *homepage*: https://trilinos.org =========== ================== =============================== version versionsuffix toolchain =========== ================== =============================== ``12.12.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``12.12.1`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` =========== ================== =============================== .. _list_software_Trim_Galore_1109: *Trim_Galore* +++++++++++++ Trim Galore is a wrapper around Cutadapt and FastQC to consistently apply adapter and quality trimming to FastQ files, with extra functionality for RRBS data. *homepage*: https://www.bioinformatics.babraham.ac.uk/projects/trim_galore/ ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``0.4.2`` ``foss/2016b`` ``0.4.4`` ``foss/2016b``, ``intel/2017a`` ``0.5.0`` ``foss/2018b`` ``0.5.0`` ``-Python-3.6.6`` ``intel/2018b`` ``0.6.0`` ``-Python-2.7.15`` ``foss/2018b`` ``0.6.0`` ``-Python-3.6.6`` ``foss/2018b`` ``0.6.1`` ``-Python-2.7.15`` ``foss/2018b`` ``0.6.1`` ``-Python-3.6.6`` ``foss/2018b`` ``0.6.2`` ``-Java-11`` ``GCCcore/8.2.0`` ``0.6.2`` ``-Python-2.7.15`` ``foss/2018b`` ``0.6.2`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================== =============================== .. _list_software_trimAl_617: *trimAl* ++++++++ EVB, FEP and LIE simulator. *homepage*: https://github.com/scapella/trimal ========= ==================== version toolchain ========= ==================== ``1.4.1`` ``GCC/8.2.0-2.31.1`` ========= ==================== .. _list_software_Trimmomatic_1158: *Trimmomatic* +++++++++++++ Trimmomatic performs a variety of useful trimming tasks for illumina paired-end and single ended data.The selection of trimming steps and their associated parameters are supplied on the command line. *homepage*: http://www.usadellab.org/cms/?page=trimmomatic ======== =================== ========== version versionsuffix toolchain ======== =================== ========== ``0.32`` ``-Java-1.7.0_80`` ``system`` ``0.36`` ``-Java-1.8.0_92`` ``system`` ``0.38`` ``-Java-1.8`` ``system`` ``0.38`` ``-Java-1.8.0_162`` ``system`` ======== =================== ========== .. _list_software_Trinity_755: *Trinity* +++++++++ Trinity represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. *homepage*: https://trinityrnaseq.github.io ========= ======================================== version toolchain ========= ======================================== ``2.2.0`` ``foss/2016a`` ``2.4.0`` ``foss/2017a`` ``2.5.1`` ``intel/2017a``, ``intel/2017b`` ``2.6.6`` ``intel/2018a`` ``2.8.4`` ``foss/2018b`` ``2.8.5`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ========= ======================================== .. _list_software_TRIQS_403: *TRIQS* +++++++ TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. *homepage*: https://triqs.github.io/triqs ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ``2.2.1`` ``-Python-2.7.15`` ``foss/2019a`` ========= ================== ============== .. _list_software_TRIQS-cthyb_986: *TRIQS-cthyb* +++++++++++++ TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. cthyb = continuous-time hybridisation-expansion quantum Monte Carlo The TRIQS-based hybridization-expansion solver allows to solve the generic problem of a quantum impurity embedded in a conduction bath for an arbitrary local interaction vertex. The “impurity” can be any set of orbitals, on one or several atoms. *homepage*: https://triqs.github.io/cthyb/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ========= ================== ============== .. _list_software_TRIQS-dft_tools_1422: *TRIQS-dft_tools* +++++++++++++++++ TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. This TRIQS-based-based application is aimed at ab-initio calculations for correlated materials, combining realistic DFT band-structure calculations with the dynamical mean-field theory. Together with the necessary tools to perform the DMFT self-consistency loop for realistic multi-band problems, the package provides a full-fledged charge self-consistent interface to the Wien2K package. In addition, if Wien2k is not available, it provides a generic interface for one-shot DFT+DMFT calculations, where only the single-particle Hamiltonian in orbital space has to be provided. *homepage*: https://triqs.github.io/dft_tools ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ========= ================== ============== .. _list_software_TRIQS-tprf_892: *TRIQS-tprf* ++++++++++++ TRIQS (Toolbox for Research on Interacting Quantum Systems) is a scientific project providing a set of C++ and Python libraries to develop new tools for the study of interacting quantum systems. TPRF is a TRIQS-based two-particle response function tool box that implements basic operations for higher order response functions such as inversion, products, the random phase approximation, the bethe salpeter equation (in the local vertex approximation), etc.. The aim is to provide efficient (C++/OpenMP/MPI) implementations of the basic operations needed to compute the two-particle response in the different two-particle channels (particle-hole, particle-particle). *homepage*: https://triqs.github.io/tprf ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ========= ================== ============== .. _list_software_TRUST_418: *TRUST* +++++++ Tcr Receptor Utilities for Solid Tissue (TRUST) is a computational tool to analyze TCR and BCR sequences using unselected RNA sequencing data, profiled from solid tissues, including tumors. *homepage*: https://bitbucket.org/liulab/trust ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``3.0.2`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============== .. _list_software_TurboVNC_755: *TurboVNC* ++++++++++ TurboVNC is a derivative of VNC (Virtual Network Computing) that is tuned to provide peak performance for 3D and video workloads. *homepage*: https://www.turbovnc.org ========= ================= version toolchain ========= ================= ``2.2.3`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_TVB_236: *TVB* +++++ The Virtual Brain will deliver the first open simulation of the human brain based on individual large-scale connectivity. *homepage*: http://thevirtualbrain.org ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.4.1`` ``-Python-2.7.11`` ``intel/2016a`` ``1.5`` ``-Python-2.7.11`` ``intel/2016a`` ========= ================== =============== .. _list_software_tvb-data_787: *tvb-data* ++++++++++ The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. Various demonstration data for use with TVB. *homepage*: http://www.thevirtualbrain.org/ ============ ================== =============== version versionsuffix toolchain ============ ================== =============== ``1.5`` ``-Python-2.7.11`` ``intel/2016a`` ``20150915`` ``-Python-2.7.11`` ``intel/2016a`` ============ ================== =============== .. _list_software_TVB-deps_709: *TVB-deps* ++++++++++ Bundle of dependency Python packages for TVB (The Virtual Brain) *homepage*: http://thevirtualbrain.org ============ ================== =============== version versionsuffix toolchain ============ ================== =============== ``20160618`` ``-Python-2.7.11`` ``intel/2016a`` ============ ================== =============== .. _list_software_tvb-framework_1351: *tvb-framework* +++++++++++++++ The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. TVB Scientific Library is the most important scientific contribution of TVB Project. *homepage*: http://www.thevirtualbrain.org/ ============ ================== =============== version versionsuffix toolchain ============ ================== =============== ``1.5`` ``-Python-2.7.11`` ``intel/2016a`` ``20150921`` ``-Python-2.7.11`` ``intel/2016a`` ============ ================== =============== .. _list_software_tvb-library_1134: *tvb-library* +++++++++++++ The Virtual Brain Project (TVB Project) has the purpose of offering some modern tools to the Neurosciences community, for computing, simulating and analyzing functional and structural data of human brains. TVB Scientific Library is the most important scientific contribution of TVB Project. *homepage*: http://www.thevirtualbrain.org/ ============ ================== =============== version versionsuffix toolchain ============ ================== =============== ``1.5`` ``-Python-2.7.11`` ``intel/2016a`` ``20150922`` ``-Python-2.7.11`` ``intel/2016a`` ============ ================== =============== .. _list_software_letter_u: *U* --- :ref:`list_software_UCLUST_480` - :ref:`list_software_UCX_240` - :ref:`list_software_udocker_749` - :ref:`list_software_UDUNITS_556` - :ref:`list_software_UFL_231` - :ref:`list_software_UMI-tools_841` - :ref:`list_software_umis_446` - :ref:`list_software_UNAFold_617` - :ref:`list_software_Unicycler_942` - :ref:`list_software_unixODBC_732` - :ref:`list_software_unrar_552` - :ref:`list_software_UnZip_502` - :ref:`list_software_USEARCH_523` - :ref:`list_software_USPEX_405` - :ref:`list_software_utf8proc_827` - :ref:`list_software_util-linux_1051` .. _list_software_UCLUST_480: *UCLUST* ++++++++ UCLUST: Extreme high-speed sequence clustering, alignment and database search. *homepage*: http://www.drive5.com/usearch/index.html =========== =============== ========== version versionsuffix toolchain =========== =============== ========== ``1.2.22q`` ``-i86linux64`` ``system`` =========== =============== ========== .. _list_software_UCX_240: *UCX* +++++ Unified Communication X An open-source production grade communication framework for data centric and high-performance applications *homepage*: http://www.openucx.org/ ============ ============= ======================================================= version versionsuffix toolchain ============ ============= ======================================================= ``1.3.1`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``1.5.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ``1.5.0rc1`` ``-hpcx`` ``GCCcore/8.2.0`` ``1.5.1`` ``GCCcore/8.2.0`` ``1.6.1`` ``GCCcore/8.3.0`` ============ ============= ======================================================= .. _list_software_udocker_749: *udocker* +++++++++ A basic user tool to execute simple docker containers in batch or interactive systems without root privileges. *homepage*: https://github.com/indigo-dc/udocker ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``1.1.1`` ``-Python-2.7.14`` ``foss/2017b`` ``1.1.3`` ``-Python-2.7.14`` ``intel/2018a`` ========= ================== =============== .. _list_software_UDUNITS_556: *UDUNITS* +++++++++ UDUNITS supports conversion of unit specifications between formatted and binary forms, arithmetic manipulation of units, and conversion of values between compatible scales of measurement. *homepage*: http://www.unidata.ucar.edu/software/udunits/ ========== ======================================================================================================================================== version toolchain ========== ======================================================================================================================================== ``2.2.20`` ``foss/2016a``, ``intel/2016b`` ``2.2.24`` ``intel/2017a`` ``2.2.25`` ``foss/2017b``, ``intel/2017b`` ``2.2.26`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2018a``, ``foss/2018b``, ``intel/2017b``, ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ========== ======================================================================================================================================== .. _list_software_UFL_231: *UFL* +++++ The Unified Form Language (UFL) is a domain specific language for declaration of finite element discretizations of variational forms. More precisely, it defines a flexible interface for choosing finite element spaces and defining expressions for weak forms in a notation close to mathematical notation. *homepage*: https://bitbucket.org/fenics-project/ufl ============ ================= ============== version versionsuffix toolchain ============ ================= ============== ``2018.1.0`` ``-Python-3.6.4`` ``foss/2018a`` ============ ================= ============== .. _list_software_UMI-tools_841: *UMI-tools* +++++++++++ Tools for handling Unique Molecular Identifiers in NGS data sets *homepage*: https://umi-tools.readthedocs.io ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``1.0.0`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== .. _list_software_umis_446: *umis* ++++++ Package for estimating UMI counts in Transcript Tag Counting data. *homepage*: https://github.com/vals/umis ========= =============== version toolchain ========= =============== ``1.0.3`` ``intel/2019a`` ========= =============== .. _list_software_UNAFold_617: *UNAFold* +++++++++ The UNAFold package contains several programs for performing energy minimization and partition function calculations on nucleic acid sequences. *homepage*: http://mfold.rna.albany.edu/?q=DINAMelt/software ======= ================ =============== version versionsuffix toolchain ======= ================ =============== ``3.8`` ``-Perl-5.24.1`` ``intel/2017a`` ======= ================ =============== .. _list_software_Unicycler_942: *Unicycler* +++++++++++ Unicycler is an assembly pipeline for bacterial genomes. It can assemble Illumina-only read sets where it functions as a SPAdes-optimiser. It can also assembly long-read-only sets (PacBio or Nanopore) where it runs a miniasm+Racon pipeline. *homepage*: ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``0.4.7`` ``-Python-3.7.2`` ``foss/2019a`` ========= ================= ============== .. _list_software_unixODBC_732: *unixODBC* ++++++++++ unixODBC provides a uniform interface between application and database driver *homepage*: https://www.unixodbc.org ========= ============== version toolchain ========= ============== ``2.3.7`` ``foss/2018b`` ========= ============== .. _list_software_unrar_552: *unrar* +++++++ RAR is a powerful archive manager. *homepage*: https://www.rarlab.com/ ========= ================= version toolchain ========= ================= ``5.6.1`` ``GCCcore/7.3.0`` ``5.7.3`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_UnZip_502: *UnZip* +++++++ UnZip is an extraction utility for archives compressed in .zip format (also called "zipfiles"). Although highly compatible both with PKWARE's PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP's own Zip program, our primary objectives have been portability and non-MSDOS functionality. *homepage*: http://www.info-zip.org/UnZip.html ======= ======================================================= version toolchain ======= ======================================================= ``6.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0`` ======= ======================================================= .. _list_software_USEARCH_523: *USEARCH* +++++++++ USEARCH is a unique sequence analysis tool which offers search and clustering algorithms that are often orders of magnitude faster than BLAST. *homepage*: http://www.drive5.com/usearch/index.html =================== =============== ========== version versionsuffix toolchain =================== =============== ========== ``5.2.236`` ``-i86linux32`` ``system`` ``5.2.236-6.1.544`` ``-i86linux32`` ``system`` ``6.1.544`` ``-i86linux32`` ``system`` =================== =============== ========== .. _list_software_USPEX_405: *USPEX* +++++++ USPEX (Universal Structure Predictor: Evolutionary Xtallography... and in Russian "uspekh" means "success" - owing to the high success rate and many useful results produced by this method) is a method developed by the Oganov laboratory since 2004. The problem of crystal structure prediction is very old and does, in fact, constitute the central problem of theoretical crystal chemistry. USPEX can also be used for finding low-energy metastable phases, as well as stable structures of nanoparticles, surface reconstructions, molecular packings in organic crystals, and for searching for materials with desired physical (mechanical, electronic) properties. The USPEX code is based on an efficient evolutionary algorithm developed by A.R. Oganov's group, but also has options for using alternative methods (random sampling, metadynamics, corrected particle swarm optimization algorithms). USPEX is interfaced with many ab initio codes, such as VASP, SIESTA, GULP, Quantum Espresso, CP2K, CASTEP, LAMMPS, and so on. *homepage*: http://uspex-team.org/uspex/overview ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``9.4.4`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== .. _list_software_utf8proc_827: *utf8proc* ++++++++++ utf8proc is a small, clean C library that provides Unicode normalization, case-folding, and other operations for data in the UTF-8 encoding. *homepage*: https://github.com/JuliaStrings/utf8proc ========= ================= version toolchain ========= ================= ``2.2.0`` ``GCCcore/6.4.0`` ``2.3.0`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_util-linux_1051: *util-linux* ++++++++++++ Set of Linux utilities *homepage*: https://www.kernel.org/pub/linux/utils/util-linux ========== ==================================== version toolchain ========== ==================================== ``2.27.1`` ``foss/2016a``, ``intel/2016a`` ``2.28`` ``foss/2016a``, ``intel/2016a`` ``2.28.1`` ``intel/2016b`` ``2.29`` ``foss/2016b``, ``intel/2016b`` ``2.29.2`` ``GCCcore/6.3.0``, ``intel/2017a`` ``2.30`` ``GCCcore/6.4.0`` ``2.30.1`` ``GCCcore/6.3.0``, ``foss/2017a`` ``2.31`` ``GCCcore/6.4.0`` ``2.31.1`` ``GCCcore/6.4.0`` ``2.32`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0`` ``2.32.1`` ``GCCcore/7.3.0`` ``2.33`` ``GCCcore/8.2.0`` ``2.34`` ``GCCcore/8.3.0`` ========== ==================================== .. _list_software_letter_v: *V* --- :ref:`list_software_V8_142` - :ref:`list_software_Valgrind_823` - :ref:`list_software_Vampir_623` - :ref:`list_software_VarDict_685` - :ref:`list_software_VariantMetaCaller_1711` - :ref:`list_software_VarScan_686` - :ref:`list_software_vartools_890` - :ref:`list_software_VASP_314` - :ref:`list_software_VAtools_712` - :ref:`list_software_VCF-kit_596` - :ref:`list_software_vcfnp_541` - :ref:`list_software_VCFtools_784` - :ref:`list_software_VEGAS_374` - :ref:`list_software_Velvet_630` - :ref:`list_software_VEP_235` - :ref:`list_software_verifyBamID_1074` - :ref:`list_software_VERSE_389` - :ref:`list_software_ViennaRNA_834` - :ref:`list_software_Vim_300` - :ref:`list_software_VirSorter_944` - :ref:`list_software_VirtualGL_890` - :ref:`list_software_VMD_231` - :ref:`list_software_Voro++_508` - :ref:`list_software_vsc-base_788` - :ref:`list_software_vsc-install_1136` - :ref:`list_software_vsc-mympirun_1274` - :ref:`list_software_vsc-mympirun-scoop_1867` - :ref:`list_software_vsc-processcontrol_1913` - :ref:`list_software_VSEARCH_524` - :ref:`list_software_vt_234` - :ref:`list_software_VTK_245` - :ref:`list_software_VTune_498` - :ref:`list_software_VV_172` - :ref:`list_software_VXL_250` .. _list_software_V8_142: *V8* ++++ R interface to Google's open source JavaScript engine *homepage*: https://cran.r-project.org/web/packages/V8/ ======= ============= ============== version versionsuffix toolchain ======= ============= ============== ``2.2`` ``-R-3.5.1`` ``foss/2018b`` ======= ============= ============== .. _list_software_Valgrind_823: *Valgrind* ++++++++++ Valgrind: Debugging and profiling tools *homepage*: http://valgrind.org ========== ================================================================================= version toolchain ========== ================================================================================= ``3.11.0`` ``foss/2016a``, ``intel/2016a`` ``3.13.0`` ``foss/2017b``, ``foss/2018a``, ``intel/2017a``, ``intel/2017b``, ``intel/2018a`` ``3.14.0`` ``foss/2018b`` ========== ================================================================================= .. _list_software_Vampir_623: *Vampir* ++++++++ The Vampir software tool provides an easy-to-use framework that enables developers to quickly display and analyze arbitrary program behavior at any level of detail. The tool suite implements optimized event analysis algorithms and customizable displays that enable fast and interactive rendering of very complex performance monitoring data. *homepage*: http://www.vampir.eu ========= ============= ========== version versionsuffix toolchain ========= ============= ========== ``8.4.1`` ``system`` ``8.4.1`` ``-demo`` ``system`` ========= ============= ========== .. _list_software_VarDict_685: *VarDict* +++++++++ VarDict is an ultra sensitive variant caller for both single and paired sample variant calling from BAM files. *homepage*: https://github.com/AstraZeneca-NGS/VarDict ========= ================ ============== version versionsuffix toolchain ========= ================ ============== ``1.5.7`` ``-Perl-5.28.0`` ``foss/2018b`` ========= ================ ============== .. _list_software_VariantMetaCaller_1711: *VariantMetaCaller* +++++++++++++++++++ VariantMetaCaller automatically integrates variant calling pipelines into a better performing overall model that also predicts accurate variant probabilities. *homepage*: http://bioinformatics.mit.bme.hu/VariantMetaCaller/ ======= =============== version toolchain ======= =============== ``1.0`` ``intel/2017a`` ======= =============== .. _list_software_VarScan_686: *VarScan* +++++++++ Variant calling and somatic mutation/CNV detection for next-generation sequencing data *homepage*: https://github.com/dkoboldt/varscan ========= ================== ========== version versionsuffix toolchain ========= ================== ========== ``2.3.6`` ``-Java-1.7.0_80`` ``system`` ``2.4.1`` ``-Java-1.7.0_80`` ``system`` ========= ================== ========== .. _list_software_vartools_890: *vartools* ++++++++++ Command line utility that provides tools for processing and analyzing astronomical time series data. *homepage*: https://www.astro.princeton.edu/~jhartman/vartools.html ======== =============================== version toolchain ======== =============================== ``1.35`` ``foss/2016b``, ``intel/2016b`` ======== =============================== .. _list_software_VASP_314: *VASP* ++++++ The Vienna Ab initio Simulation Package (VASP) is a computer program for atomic scale materials modelling, e.g. electronic structure calculations and quantum-mechanical molecular dynamics, from first principles. *homepage*: http://www.vasp.at ========= ========================= version toolchain ========= ========================= ``5.4.1`` ``intel/2016.02-GCC-4.9`` ========= ========================= .. _list_software_VAtools_712: *VAtools* +++++++++ VAtools is a python package that includes several tools to annotate VCF files with data from other tools. *homepage*: https://vatools.readthedocs.io/en/latest/ ========= ================= ============== version versionsuffix toolchain ========= ================= ============== ``3.0.1`` ``-Python-3.6.6`` ``foss/2018b`` ========= ================= ============== .. _list_software_VCF-kit_596: *VCF-kit* +++++++++ VCF-kit is a command-line based collection of utilities for performing analysis on Variant Call Format (VCF) files. *homepage*: https://github.com/AndersenLab/VCF-kit ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``0.1.6`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============== .. _list_software_vcfnp_541: *vcfnp* +++++++ Load data from a VCF (variant call format) file into numpy arrays, and (optionally) from there into an HDF5 file. *homepage*: https://github.com/alimanfoo/vcfnp ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.3.0`` ``-Python-2.7.11`` ``foss/2016a`` ========= ================== ============== .. _list_software_VCFtools_784: *VCFtools* ++++++++++ The aim of VCFtools is to provide easily accessible methods for working with complex genetic variation data in the form of VCF files. *homepage*: https://vcftools.github.io ========== ================ =============================== version versionsuffix toolchain ========== ================ =============================== ``0.1.14`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` ``0.1.15`` ``-Perl-5.24.0`` ``foss/2016b`` ``0.1.15`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``0.1.15`` ``-Perl-5.26.1`` ``foss/2018a`` ``0.1.16`` ``-Perl-5.28.0`` ``foss/2018b``, ``intel/2018b`` ========== ================ =============================== .. _list_software_VEGAS_374: *VEGAS* +++++++ VEGAS (Versatile Gene-based Association Study) is a free program for performing gene-based tests for association using the results from genetic association studies *homepage*: http://gump.qimr.edu.au/VEGAS/ ========== ========== version toolchain ========== ========== ``0.8.27`` ``system`` ========== ========== .. _list_software_Velvet_630: *Velvet* ++++++++ Sequence assembler for very short reads *homepage*: http://www.ebi.ac.uk/~zerbino/velvet/ ========== ================ ============================== version versionsuffix toolchain ========== ================ ============================== ``1.2.10`` ``-mt-kmer_191`` ``foss/2018a``, ``foss/2018b`` ``1.2.10`` ``-mt-kmer_37`` ``intel/2017a`` ========== ================ ============================== .. _list_software_VEP_235: *VEP* +++++ Variant Effect Predictor (VEP) determines the effect of your variants (SNPs, insertions, deletions, CNVs or structural variants) on genes, transcripts, and protein sequence, as well as regulatory regions. Includes EnsEMBL-XS, which provides pre-compiled replacements for frequently used routines in VEP. *homepage*: https://www.ensembl.org/info/docs/tools/vep ======== ================ =============================== version versionsuffix toolchain ======== ================ =============================== ``93.4`` ``-Perl-5.26.1`` ``intel/2018a`` ``94.0`` ``-Perl-5.28.0`` ``foss/2018b`` ``94.5`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``95.0`` ``-Perl-5.28.0`` ``foss/2018b`` ``96.0`` ``-Perl-5.28.1`` ``foss/2019a`` ======== ================ =============================== .. _list_software_verifyBamID_1074: *verifyBamID* +++++++++++++ verifyBamID is a software that verifies whether the reads in particular file match previously known genotypes for an individual (or group of individuals), and checks whether the reads are contaminated as a mixture of two samples. verifyBamID can detect sample contamination and swaps when external genotypes are available. When external genotypes are not available, verifyBamID still robustly detects sample swaps. *homepage*: http://csg.sph.umich.edu/kang/verifyBamID/index.html ========= ============== version toolchain ========= ============== ``1.1.3`` ``foss/2016a`` ========= ============== .. _list_software_VERSE_389: *VERSE* +++++++ A versatile and efficient RNA-Seq read counting tool *homepage*: https://github.com/qinzhu/VERSE ========= ============== version toolchain ========= ============== ``0.1.5`` ``foss/2016b`` ========= ============== .. _list_software_ViennaRNA_834: *ViennaRNA* +++++++++++ The Vienna RNA Package consists of a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. *homepage*: https://www.tbi.univie.ac.at/RNA/ ========== ================== =============================== version versionsuffix toolchain ========== ================== =============================== ``2.2.3`` ``intel/2016b`` ``2.3.4`` ``foss/2016b`` ``2.3.5`` ``intel/2017a`` ``2.4.10`` ``-Python-2.7.15`` ``foss/2018b``, ``intel/2018b`` ``2.4.11`` ``-Python-3.6.6`` ``foss/2018b`` ``2.4.14`` ``-Python-3.6.6`` ``foss/2018b`` ========== ================== =============================== .. _list_software_Vim_300: *Vim* +++++ Vim is an advanced text editor that seeks to provide the power of the de-facto Unix editor 'Vi', with a more complete feature set. *homepage*: http://www.vim.org ============ ================== ================= version versionsuffix toolchain ============ ================== ================= ``8.0`` ``-Python-2.7.11`` ``foss/2016a`` ``8.1.0483`` ``-Python-2.7.15`` ``foss/2018b`` ``8.1.1209`` ``-Python-3.7.2`` ``GCCcore/8.2.0`` ============ ================== ================= .. _list_software_VirSorter_944: *VirSorter* +++++++++++ VirSorter: mining viral signal from microbial genomic data. *homepage*: https://github.com/simroux/VirSorter ============ ================ ============== version versionsuffix toolchain ============ ================ ============== ``20160601`` ``-Perl-5.22.1`` ``foss/2016a`` ============ ================ ============== .. _list_software_VirtualGL_890: *VirtualGL* +++++++++++ VirtualGL is an open source toolkit that gives any Linux or Unix remote display software the ability to run OpenGL applications with full hardware acceleration. *homepage*: https://virtualgl.org/ ========= ============== version toolchain ========= ============== ``2.6.1`` ``foss/2018b`` ========= ============== .. _list_software_VMD_231: *VMD* +++++ VMD is a molecular visualization program for displaying, animating, and analyzing large biomolecular systems using 3-D graphics and built-in scripting. *homepage*: http://www.ks.uiuc.edu/Research/vmd ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``1.9.3`` ``-Python-2.7.12`` ``intel/2016b`` ``1.9.3`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2018a`` ``1.9.3`` ``-Python-2.7.15`` ``intel/2018b`` ========= ================== =============================== .. _list_software_Voro++_508: *Voro++* ++++++++ Voro++ is a software library for carrying out three-dimensional computations of the Voronoi tessellation. A distinguishing feature of the Voro++ library is that it carries out cell-based calculations, computing the Voronoi cell for each particle individually. It is particularly well-suited for applications that rely on cell-based statistics, where features of Voronoi cells (eg. volume, centroid, number of faces) can be used to analyze a system of particles. *homepage*: http://math.lbl.gov/voro++/ ========= ================================================== version toolchain ========= ================================================== ``0.4.6`` ``GCCcore/6.4.0``, ``foss/2016a``, ``intel/2016a`` ========= ================================================== .. _list_software_vsc-base_788: *vsc-base* ++++++++++ Basic Python libraries used by UGent's HPC group *homepage*: http://hpcugent.github.com/vsc-base/ ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``1.6.9`` ``system`` ``1.7.3`` ``system`` ``2.0.4`` ``system`` ``2.1.2`` ``system`` ``2.4.2`` ``system`` ``2.4.17`` ``-Python-2.7.11`` ``intel/2016a`` ``2.5.1`` ``system`` ``2.5.1`` ``-Python-2.7.11`` ``intel/2016a`` ``2.5.1`` ``-Python-2.7.12`` ``intel/2016b`` ``2.5.8`` ``system`` ``2.8.0`` ``system`` ``2.8.1`` ``system`` ``2.8.3`` ``system`` ========== ================== =============== .. _list_software_vsc-install_1136: *vsc-install* +++++++++++++ vsc-install provides shared setuptools functions and classes for Python libraries developed by UGent's HPC group *homepage*: https://pypi.python.org/pypi/vsc-install =========== ================== =============== version versionsuffix toolchain =========== ================== =============== ``0.9.18`` ``-Python-2.7.11`` ``intel/2016a`` ``0.10.6`` ``system`` ``0.10.6`` ``-Python-2.7.11`` ``intel/2016a`` ``0.10.11`` ``-Python-2.7.11`` ``intel/2016a`` ``0.10.11`` ``-Python-2.7.12`` ``intel/2016b`` ``0.10.25`` ``system`` ``0.10.26`` ``system`` ``0.11.1`` ``system`` ``0.11.2`` ``system`` =========== ================== =============== .. _list_software_vsc-mympirun_1274: *vsc-mympirun* ++++++++++++++ mympirun is a tool to make it easier for users of HPC clusters to run MPI programs with good performance. *homepage*: https://github.com/hpcugent/vsc-mympirun =========== ================================== =============== version versionsuffix toolchain =========== ================================== =============== ``3.2.1`` ``system`` ``3.3.0`` ``system`` ``3.4.2`` ``system`` ``3.4.2`` ``-Python-2.7.11-vsc-base-2.4.17`` ``intel/2016a`` ``3.4.2`` ``-Python-2.7.11-vsc-base-2.5.1`` ``intel/2016a`` ``3.4.2`` ``-vsc-base-2.4.2`` ``system`` ``3.4.3`` ``-Python-2.7.12`` ``intel/2016b`` ``4.0.0`` ``system`` ``4.0.0b0`` ``system`` ``4.0.1`` ``system`` ``4.0.2`` ``system`` ``4.1.4`` ``system`` ``4.1.5`` ``system`` ``4.1.6`` ``system`` ``4.1.8`` ``system`` ``4.1.9`` ``system`` =========== ================================== =============== .. _list_software_vsc-mympirun-scoop_1867: *vsc-mympirun-scoop* ++++++++++++++++++++ VSC-tools is a set of Python libraries and scripts that are commonly used within HPC-UGent. *homepage*: http://hpcugent.github.com/vsc-mympirun/ ========= ================== =============== version versionsuffix toolchain ========= ================== =============== ``3.4.1`` ``-Python-2.7.12`` ``intel/2016b`` ========= ================== =============== .. _list_software_vsc-processcontrol_1913: *vsc-processcontrol* ++++++++++++++++++++ vsc-processcontrol is a module to abstract process control like scheduler settings and affinity from actual implementations like vsc.affinity and psutil. *homepage*: http://hpcugent.github.com/vsc-processcontrol/ ======= =================== ========== version versionsuffix toolchain ======= =================== ========== ``1.0`` ``system`` ``1.0`` ``-vsc-base-2.1.2`` ``system`` ======= =================== ========== .. _list_software_VSEARCH_524: *VSEARCH* +++++++++ VSEARCH supports de novo and reference based chimera detection, clustering, full-length and prefix dereplication, rereplication, reverse complementation, masking, all-vs-all pairwise global alignment, exact and global alignment searching, shuffling, subsampling and sorting. It also supports FASTQ file analysis, filtering, conversion and merging of paired-end reads. *homepage*: https://github.com/torognes/vsearch ========== ======================================== version toolchain ========== ======================================== ``2.9.1`` ``foss/2018b`` ``2.13.4`` ``iccifort/2019.1.144-GCC-8.2.0-2.31.1`` ========== ======================================== .. _list_software_vt_234: *vt* ++++ A tool set for short variant discovery in genetic sequence data. *homepage*: http://genome.sph.umich.edu/wiki/Vt =========== ============== version toolchain =========== ============== ``0.57721`` ``foss/2018b`` =========== ============== .. _list_software_VTK_245: *VTK* +++++ The Visualization Toolkit (VTK) is an open-source, freely available software system for 3D computer graphics, image processing and visualization. VTK consists of a C++ class library and several interpreted interface layers including Tcl/Tk, Java, and Python. VTK supports a wide variety of visualization algorithms including: scalar, vector, tensor, texture, and volumetric methods; and advanced modeling techniques such as: implicit modeling, polygon reduction, mesh smoothing, cutting, contouring, and Delaunay triangulation. *homepage*: https://www.vtk.org ========= ================== ================================== version versionsuffix toolchain ========= ================== ================================== ``6.3.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``6.3.0`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``7.0.0`` ``-Python-2.7.12`` ``intel/2016b`` ``7.1.0`` ``-Python-2.7.12`` ``intel/2016b`` ``7.1.1`` ``-Python-2.7.13`` ``intel/2017a`` ``8.0.1`` ``-Python-2.7.14`` ``foss/2017b``, ``intel/2017b`` ``8.1.0`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2018a`` ``8.1.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``8.1.1`` ``-Python-2.7.14`` ``intel/2018a`` ``8.1.1`` ``-Python-2.7.15`` ``foss/2018b`` ``8.1.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ``8.2.0`` ``-Python-2.7.15`` ``foss/2019a`` ``8.2.0`` ``-Python-3.7.2`` ``foss/2019a``, ``intel/2019a`` ``8.2.0`` ``-Python-3.7.4`` ``foss/2019b`` ========= ================== ================================== .. _list_software_VTune_498: *VTune* +++++++ Intel VTune Amplifier XE is the premier performance profiler for C, C++, C#, Fortran, Assembly and Java. *homepage*: https://software.intel.com/en-us/vtune ================= ========== version toolchain ================= ========== ``2013_update6`` ``system`` ``2013_update8`` ``system`` ``2013_update9`` ``system`` ``2013_update10`` ``system`` ``2013_update11`` ``system`` ``2013_update12`` ``system`` ``2016_update3`` ``system`` ``2017`` ``system`` ``2017_update1`` ``system`` ``2017_update2`` ``system`` ``2017_update3`` ``system`` ``2018_update1`` ``system`` ``2018_update2`` ``system`` ``2018_update3`` ``system`` ``2019_update2`` ``system`` ``2019_update3`` ``system`` ``2019_update5`` ``system`` ================= ========== .. _list_software_VV_172: *VV* ++++ VV is an open-source and cross platform image viewer, designed for fast and simple visualization of spatio-temporal images: 2D, 2D+t, 3D and 3D+t (or 4D) images. Only the command-line (clitk) tools are build. *homepage*: https://www.creatis.insa-lyon.fr/rio/vv ============== ================= ============== version versionsuffix toolchain ============== ================= ============== ``2018.09.19`` ``-Python-3.6.6`` ``foss/2018b`` ============== ================= ============== .. _list_software_VXL_250: *VXL* +++++ A multi-platform collection of C++ software libraries for Computer Vision and Image Understanding. *homepage*: https://sf.net/projects/vxl ========== ============== version toolchain ========== ============== ``1.18.0`` ``foss/2018a`` ========== ============== .. _list_software_letter_w: *W* --- :ref:`list_software_Wannier90_829` - :ref:`list_software_WannierTools_1253` - :ref:`list_software_wcwidth_762` - :ref:`list_software_WebKitGTK+_855` - :ref:`list_software_WebSocket++_989` - :ref:`list_software_WEKA_296` - :ref:`list_software_wget_439` - :ref:`list_software_wheel_533` - :ref:`list_software_WIEN2k_464` - :ref:`list_software_WISExome_753` - :ref:`list_software_wkhtmltopdf_1204` - :ref:`list_software_worker_666` - :ref:`list_software_WPS_250` - :ref:`list_software_WRF_239` - :ref:`list_software_WRF-Fire_674` - :ref:`list_software_wrf-python_1054` - :ref:`list_software_wxPropertyGrid_1498` - :ref:`list_software_wxPython_881` - :ref:`list_software_wxWidgets_966` .. _list_software_Wannier90_829: *Wannier90* +++++++++++ A tool for obtaining maximally-localised Wannier functions *homepage*: http://www.wannier.org =========== ============= ================================================ version versionsuffix toolchain =========== ============= ================================================ ``1.2`` ``intel/2016.02-GCC-4.9`` ``2.0.1`` ``intel/2016.02-GCC-4.9``, ``intel/2016a`` ``2.0.1.1`` ``-abinit`` ``intel/2018b`` ``2.1.0`` ``foss/2017b``, ``intel/2017a``, ``intel/2017b`` ``3.0.0`` ``intel/2018b`` =========== ============= ================================================ .. _list_software_WannierTools_1253: *WannierTools* ++++++++++++++ an open-source software package for novel topological materials *homepage*: http://www.wanniertools.com/ ========= =============== version toolchain ========= =============== ``2.3.0`` ``intel/2018a`` ========= =============== .. _list_software_wcwidth_762: *wcwidth* +++++++++ wcwidth is a low-level Python library to simplify Terminal emulation. *homepage*: https://github.com/jquast/wcwidth ========= ================== =============================== version versionsuffix toolchain ========= ================== =============================== ``0.1.7`` ``-Python-2.7.11`` ``foss/2016a`` ``0.1.7`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``0.1.7`` ``-Python-3.5.1`` ``foss/2016a`` ``0.1.7`` ``-Python-3.5.2`` ``intel/2016b`` ========= ================== =============================== .. _list_software_WebKitGTK+_855: *WebKitGTK+* ++++++++++++ WebKitGTK+ is a full-featured port of the WebKit rendering engine, suitable for projects requiring any kind of web integration, from hybrid HTML/CSS applications to full-fledged web browsers. It offers WebKit’s full functionality and is useful in a wide range of systems from desktop computers to embedded systems like phones, tablets, and televisions. *homepage*: https://webkitgtk.org/ ========== ==================== version toolchain ========== ==================== ``2.24.1`` ``GCC/8.2.0-2.31.1`` ========== ==================== .. _list_software_WebSocket++_989: *WebSocket++* +++++++++++++ WebSocket++ is an open source (BSD license) header only C++ library that implements RFC6455 The WebSocket Protocol. *homepage*: https://www.zaphoyd.com/websocketpp/ ========= =============== version toolchain ========= =============== ``0.8.1`` ``gompi/2019a`` ========= =============== .. _list_software_WEKA_296: *WEKA* ++++++ Weka is a collection of machine learning algorithms for data mining tasks. The algorithms can either be applied directly to a dataset or called from your own Java code. Weka contains tools for data pre-processing, classification, regression, clustering, association rules, and visualization. It is also well-suited for developing new machine learning schemes. *homepage*: http://www.cs.waikato.ac.nz/ml/weka/index.html ========== ================== ========== version versionsuffix toolchain ========== ================== ========== ``3.6.12`` ``-Java-1.7.0_80`` ``system`` ``3.7.0`` ``-Java-1.7.0_80`` ``system`` ========== ================== ========== .. _list_software_wget_439: *wget* ++++++ GNU Wget is a free software package for retrieving files using HTTP, HTTPS and FTP, the most widely-used Internet protocols. It is a non-interactive commandline tool, so it may easily be called from scripts, cron jobs, terminals without X-Windows support, etc. *homepage*: https://www.gnu.org/software/wget/ ========== ============================== version toolchain ========== ============================== ``1.17.1`` ``foss/2016a``, ``foss/2016b`` ``1.19.4`` ``GCCcore/6.4.0`` ``1.20.1`` ``GCCcore/7.3.0`` ========== ============================== .. _list_software_wheel_533: *wheel* +++++++ A built-package format for Python. *homepage*: https://pypi.python.org/pypi/wheel ========== ================== ======================================================================== version versionsuffix toolchain ========== ================== ======================================================================== ``0.29.0`` ``-Python-2.7.11`` ``foss/2016a`` ``0.29.0`` ``-Python-3.5.1`` ``foss/2016a`` ``0.30.0`` ``-Python-2.7.14`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``0.30.0`` ``-Python-3.6.3`` ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017b``, ``intelcuda/2017b`` ``0.30.0`` ``-Python-3.6.4`` ``foss/2018a``, ``intel/2018a`` ``0.31.0`` ``-Python-2.7.14`` ``fosscuda/2018a``, ``intel/2018a`` ``0.31.0`` ``-Python-3.6.4`` ``foss/2018a``, ``fosscuda/2018a`` ``0.31.1`` ``-Python-2.7.15`` ``fosscuda/2018b`` ``0.31.1`` ``-Python-3.6.6`` ``foss/2018b``, ``fosscuda/2018b`` ========== ================== ======================================================================== .. _list_software_WIEN2k_464: *WIEN2k* ++++++++ The program package WIEN2k allows to perform electronic structure calculations of solids using density functional theory (DFT). It is based on the full-potential (linearized) augmented plane-wave ((L)APW) + local orbitals (lo) method, one among the most accurate schemes for band structure calculations. WIEN2k is an all-electron scheme including relativistic effects and has many features. *homepage*: http://www.wien2k.at/ ======== ================================================ version toolchain ======== ================================================ ``17.1`` ``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` ``18.1`` ``foss/2018a``, ``gimkl/2017a``, ``intel/2018a`` ``19.1`` ``intel/2019a`` ======== ================================================ .. _list_software_WISExome_753: *WISExome* ++++++++++ A within-sample comparison approach to detect copy number variations in whole exome sequencing data *homepage*: https://github.com/VUmcCGP/wisexome ============ ================== =============== version versionsuffix toolchain ============ ================== =============== ``20180517`` ``-Python-2.7.14`` ``intel/2018a`` ============ ================== =============== .. _list_software_wkhtmltopdf_1204: *wkhtmltopdf* +++++++++++++ wkhtmltopdf and wkhtmltoimage are open source (LGPLv3) command line tools to render HTML into PDF and various image formats using the Qt WebKit rendering engine. These run entirely headless and do not require a display or display service. *homepage*: http://wkhtmltopdf.org/ ========== ================= ========== version versionsuffix toolchain ========== ================= ========== ``0.12.3`` ``-Linux-x86_64`` ``system`` ========== ================= ========== .. _list_software_worker_666: *worker* ++++++++ The Worker framework has been developed to help deal with parameter exploration experiments that would otherwise result in many jobs, forcing the user resort to scripting to retain her sanity; see also https://vscentrum.be/neutral/documentation/cluster-doc/running-jobs/worker-framework. *homepage*: https://github.com/gjbex/worker ========== ================ =============== version versionsuffix toolchain ========== ================ =============== ``1.6.4`` ``intel/2016a`` ``1.6.5`` ``intel/2016a`` ``1.6.6`` ``intel/2016b`` ``1.6.7`` ``-intel-2016b`` ``system`` ``1.6.7`` ``-intel-2017a`` ``system`` ``1.6.7`` ``-intel-2017b`` ``system`` ``1.6.8`` ``-intel-2018a`` ``system`` ``1.6.8`` ``-intel-2018b`` ``system`` ``1.6.11`` ``-intel-2019b`` ``system`` ========== ================ =============== .. _list_software_WPS_250: *WPS* +++++ WRF Preprocessing System (WPS) for WRF. The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. *homepage*: http://www.wrf-model.org ========= ============= =============== version versionsuffix toolchain ========= ============= =============== ``3.8.0`` ``-dmpar`` ``intel/2016a`` ``4.0.1`` ``-dmpar`` ``intel/2018b`` ``4.0.2`` ``-dmpar`` ``foss/2018b`` ``4.1`` ``-dmpar`` ``intel/2019b`` ========= ============= =============== .. _list_software_WRF_239: *WRF* +++++ The Weather Research and Forecasting (WRF) Model is a next-generation mesoscale numerical weather prediction system designed to serve both operational forecasting and atmospheric research needs. *homepage*: http://www.wrf-model.org ========= ============= ================================ version versionsuffix toolchain ========= ============= ================================ ``3.8.0`` ``-dmpar`` ``intel/2016a``, ``intel/2016b`` ``4.0.1`` ``-dmpar`` ``intel/2018b`` ``4.0.2`` ``-dmpar`` ``foss/2018b`` ``4.1.3`` ``-dmpar`` ``intel/2019b`` ========= ============= ================================ .. _list_software_WRF-Fire_674: *WRF-Fire* ++++++++++ WRF-Fire combines the Weather Research and Forecasting model (WRF) with a fire code implementing a surface fire behavior model, called SFIRE, based on semi-empirical formulas calculate the rate of spread of the fire line (the interface between burning and unignited fuel) based on fuel properties, wind velocities from WRF, and terrain slope. The fire spread is implemented by the level set method. *homepage*: http://www.openwfm.org/wiki/WRF-SFIRE ============ ============= =============== version versionsuffix toolchain ============ ============= =============== ``20170221`` ``-dmpar`` ``intel/2016b`` ============ ============= =============== .. _list_software_wrf-python_1054: *wrf-python* ++++++++++++ A collection of diagnostic and interpolation routines for use with output from the Weather Research and Forecasting (WRF-ARW) Model. *homepage*: https://wrf-python.readthedocs.io ========= ================= =============== version versionsuffix toolchain ========= ================= =============== ``1.2.0`` ``-Python-3.6.4`` ``intel/2018a`` ``1.3.1`` ``-Python-3.6.6`` ``intel/2018b`` ========= ================= =============== .. _list_software_wxPropertyGrid_1498: *wxPropertyGrid* ++++++++++++++++ wxPropertyGrid is a property sheet control for wxWidgets. In other words, it is a specialized two-column grid for editing properties such as strings, numbers, flagsets, string arrays, and colours. *homepage*: http://wxpropgrid.sourceforge.net/ ========== ============= version toolchain ========== ============= ``1.4.15`` ``GCC/4.9.2`` ========== ============= .. _list_software_wxPython_881: *wxPython* ++++++++++ wxPython is a GUI toolkit for the Python programming language. It allows Python programmers to create programs with a robust, highly functional graphical user interface, simply and easily. It is implemented as a Python extension module (native code) that wraps the popular wxWidgets cross platform GUI library, which is written in C++. *homepage*: http://www.wxpython.org =========== ================== =============================== version versionsuffix toolchain =========== ================== =============================== ``3.0.2.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``3.0.2.0`` ``-Python-2.7.12`` ``intel/2016b`` ``3.0.2.0`` ``-Python-2.7.13`` ``intel/2017a`` ``3.0.2.0`` ``-Python-2.7.14`` ``intel/2017b`` ``3.0.2.0`` ``-Python-2.7.15`` ``foss/2018b`` ``4.0.4`` ``-Python-2.7.15`` ``GCC/8.2.0-2.31.1`` ``4.0.4`` ``-Python-3.7.2`` ``GCC/8.2.0-2.31.1`` =========== ================== =============================== .. _list_software_wxWidgets_966: *wxWidgets* +++++++++++ wxWidgets is a C++ library that lets developers create applications for Windows, Mac OS X, Linux and other platforms with a single code base. It has popular language bindings for Python, Perl, Ruby and many other languages, and unlike other cross-platform toolkits, wxWidgets gives applications a truly native look and feel because it uses the platform's native API rather than emulating the GUI. *homepage*: https://www.wxwidgets.org ========= ==================== version toolchain ========= ==================== ``3.0.3`` ``foss/2018a`` ``3.0.4`` ``GCC/8.2.0-2.31.1`` ========= ==================== .. _list_software_letter_x: *X* --- :ref:`list_software_X11_186` - :ref:`list_software_x264_276` - :ref:`list_software_x265_277` - :ref:`list_software_xarray_663` - :ref:`list_software_xbitmaps_872` - :ref:`list_software_xcb-proto_926` - :ref:`list_software_xcb-util_808` - :ref:`list_software_xcb-util-image_1368` - :ref:`list_software_xcb-util-keysyms_1642` - :ref:`list_software_xcb-util-renderutil_1939` - :ref:`list_software_xcb-util-wm_1081` - :ref:`list_software_xCell_504` - :ref:`list_software_XCfun_484` - :ref:`list_software_XCrySDen_752` - :ref:`list_software_Xerces-C++_816` - :ref:`list_software_xextproto_1021` - :ref:`list_software_xf86vidmodeproto_1640` - :ref:`list_software_XGBoost_678` - :ref:`list_software_xineramaproto_1417` - :ref:`list_software_XKeyboardConfig_1503` - :ref:`list_software_XMDS2_366` - :ref:`list_software_Xmipp_526` - :ref:`list_software_XML-LibXML_806` - :ref:`list_software_XML-Parser_907` - :ref:`list_software_xmlf90_544` - :ref:`list_software_XMLSec_524` - :ref:`list_software_XMLStarlet_976` - :ref:`list_software_xonsh_560` - :ref:`list_software_xorg-macros_1138` - :ref:`list_software_xprop_569` - :ref:`list_software_xproto_684` - :ref:`list_software_XSD_239` - :ref:`list_software_XTandem_689` - :ref:`list_software_xtrans_672` - :ref:`list_software_XZ_178` .. _list_software_X11_186: *X11* +++++ The X Window System (X11) is a windowing system for bitmap displays *homepage*: https://www.x.org ============ ================================================== version toolchain ============ ================================================== ``20160819`` ``GCCcore/5.4.0``, ``foss/2016b``, ``intel/2016b`` ``20170129`` ``GCCcore/6.3.0``, ``gimkl/2017a`` ``20170314`` ``GCCcore/6.3.0`` ``20171023`` ``GCCcore/6.4.0`` ``20180131`` ``GCCcore/6.4.0`` ``20180604`` ``GCCcore/7.3.0`` ``20190311`` ``GCCcore/8.2.0`` ``20190717`` ``GCCcore/8.3.0`` ============ ================================================== .. _list_software_x264_276: *x264* ++++++ x264 is a free software library and application for encoding video streams into the H.264/MPEG-4 AVC compression format, and is released under the terms of the GNU GPL. *homepage*: https://www.videolan.org/developers/x264.html ============ ================================= version toolchain ============ ================================= ``20160114`` ``gimkl/2.11.5``, ``intel/2016a`` ``20160430`` ``foss/2016a``, ``intel/2016a`` ``20160614`` ``foss/2016b``, ``intel/2016b`` ``20170406`` ``gimkl/2017a`` ``20170721`` ``GCCcore/6.4.0`` ``20170913`` ``intel/2017a`` ``20171217`` ``foss/2017b``, ``intel/2017b`` ``20180128`` ``GCCcore/6.4.0`` ``20180325`` ``GCCcore/6.4.0`` ``20181203`` ``GCCcore/7.3.0`` ``20190413`` ``GCCcore/8.2.0`` ``20190925`` ``GCCcore/8.3.0`` ============ ================================= .. _list_software_x265_277: *x265* ++++++ x265 is a free software library and application for encoding video streams into the H.265 AVC compression format, and is released under the terms of the GNU GPL. *homepage*: https://x265.org/ ======= ================================== version toolchain ======= ================================== ``2.4`` ``foss/2016b`` ``2.5`` ``intel/2017a`` ``2.6`` ``GCCcore/6.4.0``, ``intel/2017b`` ``2.7`` ``GCCcore/6.4.0`` ``2.9`` ``GCCcore/7.3.0`` ``3.0`` ``GCCcore/8.2.0`` ``3.2`` ``GCCcore/8.3.0`` ======= ================================== .. _list_software_xarray_663: *xarray* ++++++++ xarray (formerly xray) is an open source project and Python package that aims to bring the labeled data power of pandas to the physical sciences, by providing N-dimensional variants of the core pandas data structures. *homepage*: https://github.com/pydata/xarray ========== ================== =============== version versionsuffix toolchain ========== ================== =============== ``0.9.5`` ``-Python-2.7.13`` ``intel/2017a`` ``0.9.5`` ``-Python-3.6.1`` ``intel/2017a`` ``0.9.6`` ``-Python-2.7.13`` ``intel/2017a`` ``0.10.0`` ``-Python-2.7.14`` ``intel/2017b`` ``0.10.0`` ``-Python-3.6.3`` ``intel/2017b`` ``0.10.3`` ``-Python-3.6.4`` ``intel/2018a`` ``0.10.4`` ``-Python-3.6.4`` ``intel/2018a`` ``0.10.8`` ``-Python-3.6.4`` ``intel/2018a`` ``0.12.1`` ``-Python-3.6.6`` ``intel/2018b`` ``0.13.0`` ``-Python-3.7.2`` ``intel/2019a`` ========== ================== =============== .. _list_software_xbitmaps_872: *xbitmaps* ++++++++++ provides bitmaps for x *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =========================================== version toolchain ========= =========================================== ``1.1.1`` ``foss/2016a``, ``intel/2016a``, ``system`` ``1.1.2`` ``system`` ========= =========================================== .. _list_software_xcb-proto_926: *xcb-proto* +++++++++++ The X protocol C-language Binding (XCB) is a replacement for Xlib featuring a small footprint, latency hiding, direct access to the protocol, improved threading support, and extensibility. *homepage*: http://xcb.freedesktop.org/ ======== ========== version toolchain ======== ========== ``1.11`` ``system`` ======== ========== .. _list_software_xcb-util_808: *xcb-util* ++++++++++ The xcb-util package provides additional extensions to the XCB library, many that were previously found in Xlib, but are not part of core X protocol *homepage*: http://xcb.freedesktop.org/ ========= =============================== version toolchain ========= =============================== ``0.4.0`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_xcb-util-image_1368: *xcb-util-image* ++++++++++++++++ The xcb-util-image package provides additional extensions to the XCB library. *homepage*: http://xcb.freedesktop.org/ ========= =============================== version toolchain ========= =============================== ``0.4.0`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_xcb-util-keysyms_1642: *xcb-util-keysyms* ++++++++++++++++++ The xcb-util-keysyms package contains a library for handling standard X key constants and conversion to/from keycodes. *homepage*: http://xcb.freedesktop.org/ ========= =============================== version toolchain ========= =============================== ``0.4.0`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_xcb-util-renderutil_1939: *xcb-util-renderutil* +++++++++++++++++++++ The xcb-util-renderutil package provides additional extensions to the XCB library. *homepage*: http://xcb.freedesktop.org/ ========= =============================== version toolchain ========= =============================== ``0.3.9`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_xcb-util-wm_1081: *xcb-util-wm* +++++++++++++ The xcb-util-wm package contains libraries which provide client and window-manager helpers for EWMH and ICCCM. *homepage*: http://xcb.freedesktop.org/ ========= =============================== version toolchain ========= =============================== ``0.4.1`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_xCell_504: *xCell* +++++++ xCell is a gene signatures-based method learned from thousands of pure cell types from various sources. *homepage*: https://github.com/dviraran/xCell ======== ============= ============== version versionsuffix toolchain ======== ============= ============== ``1.12`` ``-R-3.5.1`` ``foss/2018b`` ======== ============= ============== .. _list_software_XCfun_484: *XCfun* +++++++ XCFun is a library of DFT exchange-correlation (XC) functionals. It is based on automatic differentiation and can therefore generate arbitrary order derivatives of these functionals. *homepage*: http://dftlibs.org/xcfun/ ============ ================== =============== version versionsuffix toolchain ============ ================== =============== ``20180122`` ``-Python-2.7.14`` ``intel/2017b`` ``20190127`` ``-Python-3.7.2`` ``foss/2019a`` ============ ================== =============== .. _list_software_XCrySDen_752: *XCrySDen* ++++++++++ XCrySDen is a crystalline and molecular structure visualisation program aiming at display of isosurfaces and contours, which can be superimposed on crystalline structures and interactively rotated and manipulated. *homepage*: http://www.xcrysden.org/ ========== =============== version toolchain ========== =============== ``1.5.60`` ``intel/2019a`` ========== =============== .. _list_software_Xerces-C++_816: *Xerces-C++* ++++++++++++ Xerces-C++ is a validating XML parser written in a portable subset of C++. Xerces-C++ makes it easy to give your application the ability to read and write XML data. A shared library is provided for parsing, generating, manipulating, and validating XML documents using the DOM, SAX, and SAX2 APIs. *homepage*: https://xerces.apache.org/xerces-c/ ========= ================= version toolchain ========= ================= ``3.1.4`` ``GCCcore/6.4.0`` ``3.2.0`` ``GCCcore/7.3.0`` ``3.2.2`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_xextproto_1021: *xextproto* +++++++++++ XExtProto protocol headers. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================================== version toolchain ========= ================================================================== ``7.3.0`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2017b`` ========= ================================================================== .. _list_software_xf86vidmodeproto_1640: *xf86vidmodeproto* ++++++++++++++++++ X11 XFree86 video mode extension protocol headers. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== version toolchain ========= =============================== ``2.3.1`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_XGBoost_678: *XGBoost* +++++++++ XGBoost is an optimized distributed gradient boosting library designed to be highly efficient, flexible and portable. *homepage*: https://github.com/dmlc/xgboost ============ =================== =============== version versionsuffix toolchain ============ =================== =============== ``0.6a2`` ``-Python-2.7.12`` ``intel/2016b`` ``0.6a2`` ``-Python-3.5.2`` ``intel/2016b`` ``0.6a2`` ``-Python-3.6.1`` ``intel/2017a`` ``0.72.1`` ``-Python-2.7.14`` ``intel/2017b`` ``20171120`` ``-Java-1.8.0_152`` ``intel/2017b`` ============ =================== =============== .. _list_software_xineramaproto_1417: *xineramaproto* +++++++++++++++ X protocol and ancillary headers for xinerama *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= =============================== version toolchain ========= =============================== ``1.2.1`` ``foss/2016a``, ``intel/2016a`` ========= =============================== .. _list_software_XKeyboardConfig_1503: *XKeyboardConfig* +++++++++++++++++ The non-arch keyboard configuration database for X Window. The goal is to provide the consistent, well-structured, frequently released open source of X keyboard configuration data for X Window System implementations (free, open source and commercial). The project is targeted to XKB-based systems. *homepage*: http://www.freedesktop.org/wiki/Software/XKeyboardConfig/ ======== =============================== version toolchain ======== =============================== ``2.17`` ``foss/2016a``, ``intel/2016a`` ======== =============================== .. _list_software_XMDS2_366: *XMDS2* +++++++ The purpose of XMDS2 is to simplify the process of creating simulations that solve systems of initial-value first-order partial and ordinary differential equations. *homepage*: http://www.xmds.org/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.2.3`` ``-Python-2.7.15`` ``foss/2018b`` ========= ================== ============== .. _list_software_Xmipp_526: *Xmipp* +++++++ Scipion is an image processing framework to obtain 3D models of macromolecular complexes using Electron Microscopy (3DEM). It integrates several software packages and presents an unified interface for both biologists and developers. Scipion allows to execute workflows combining different software tools, while taking care of formats and conversions. Additionally, all steps are tracked and can be reproduced later on. *homepage*: https://github.com/I2PC/scipion/wiki ================== ================== ================================== version versionsuffix toolchain ================== ================== ================================== ``3.19.04-Apollo`` ``-Python-2.7.15`` ``foss/2019a``, ``fosscuda/2019a`` ================== ================== ================================== .. _list_software_XML-LibXML_806: *XML-LibXML* ++++++++++++ Perl binding for libxml2 *homepage*: https://metacpan.org/pod/distribution/XML-LibXML/LibXML.pod ========== ================ =============================== version versionsuffix toolchain ========== ================ =============================== ``2.0132`` ``-Perl-5.24.0`` ``foss/2016b``, ``intel/2016b`` ``2.0132`` ``-Perl-5.24.1`` ``intel/2017a`` ``2.0132`` ``-Perl-5.26.0`` ``foss/2017b``, ``intel/2017b`` ``2.0132`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` ``2.0132`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` ``2.0200`` ``-Perl-5.28.1`` ``GCCcore/8.2.0`` ``2.0201`` ``GCCcore/8.3.0`` ========== ================ =============================== .. _list_software_XML-Parser_907: *XML-Parser* ++++++++++++ This is a Perl extension interface to James Clark's XML parser, expat. *homepage*: http://search.cpan.org/~toddr/XML-Parser-2.41/ =========== ================ ====================================================================================== version versionsuffix toolchain =========== ================ ====================================================================================== ``2.41`` ``-Perl-5.20.3`` ``intel/2016a`` ``2.44`` ``-Perl-5.22.1`` ``foss/2016a``, ``intel/2016a`` ``2.44_01`` ``-Perl-5.24.0`` ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016b``, ``gimkl/2017a``, ``intel/2016b`` ``2.44_01`` ``-Perl-5.24.1`` ``GCCcore/6.3.0``, ``intel/2017a`` ``2.44_01`` ``-Perl-5.26.0`` ``GCCcore/6.4.0`` ``2.44_01`` ``-Perl-5.26.1`` ``GCCcore/6.4.0`` ``2.44_01`` ``-Perl-5.28.0`` ``GCCcore/7.3.0`` =========== ================ ====================================================================================== .. _list_software_xmlf90_544: *xmlf90* ++++++++ xmlf90 is a basic XML parsing library written in Fortran. *homepage*: https://launchpad.net/xmlf90 ========= ============================== version toolchain ========= ============================== ``1.5.3`` ``foss/2016b``, ``foss/2017a`` ========= ============================== .. _list_software_XMLSec_524: *XMLSec* ++++++++ XML Security Library is a C library based on LibXML2, supporting major XML security standards. *homepage*: https://www.aleksey.com/xmlsec/index.html ========== ================= version toolchain ========== ================= ``1.2.26`` ``GCCcore/6.4.0`` ========== ================= .. _list_software_XMLStarlet_976: *XMLStarlet* ++++++++++++ Command line XML tool *homepage*: http://xmlstar.sourceforge.net ========= ================================= version toolchain ========= ================================= ``1.6.1`` ``GCCcore/6.4.0``, ``foss/2016a`` ========= ================================= .. _list_software_xonsh_560: *xonsh* +++++++ Xonsh is a Python-ish, BASHwards-looking shell language and command prompt. *homepage*: http://xon.sh/ ========= =============== version toolchain ========= =============== ``0.3.2`` ``intel/2016a`` ========= =============== .. _list_software_xorg-macros_1138: *xorg-macros* +++++++++++++ X.org macros utilities. *homepage*: https://cgit.freedesktop.org/xorg/util/macros ========== ============================================================================================= version toolchain ========== ============================================================================================= ``1.19.0`` ``foss/2016a``, ``foss/2016b``, ``gimkl/2.11.5``, ``intel/2016a``, ``intel/2016b`` ``1.19.1`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0`` ``1.19.2`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` ========== ============================================================================================= .. _list_software_xprop_569: *xprop* +++++++ The xprop utility is for displaying window and font properties in an X server. One window or font is selected using the command line arguments or possibly in the case of a window, by clicking on the desired window. A list of properties is then given, possibly with formatting information. *homepage*: https://www.x.org/wiki/ ========= ================= ======================================================================================================================= version versionsuffix toolchain ========= ================= ======================================================================================================================= ``1.2.2`` ``GCCcore/5.4.0``, ``GCCcore/6.4.0``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ``1.2.2`` ``-X11-20180131`` ``GCCcore/6.4.0`` ``1.2.3`` ``GCCcore/7.3.0`` ``1.2.4`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ================= ======================================================================================================================= .. _list_software_xproto_684: *xproto* ++++++++ X protocol and ancillary headers *homepage*: https://www.freedesktop.org/wiki/Software/xlibs ========== ========================================================================== version toolchain ========== ========================================================================== ``7.0.28`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ``7.0.29`` ``intel/2016a`` ``7.0.31`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.3.0`` ========== ========================================================================== .. _list_software_XSD_239: *XSD* +++++ CodeSynthesis XSD is an open-source, cross-platform W3C XML Schema to C++ data binding compiler. *homepage*: https://www.codesynthesis.com/products/xsd/ ========= ================= version toolchain ========= ================= ``4.0.0`` ``GCCcore/8.2.0`` ========= ================= .. _list_software_XTandem_689: *XTandem* +++++++++ X!Tandem open source is software that can match tandem mass spectra with peptide sequences, in a process that has come to be known as protein identification. *homepage*: https://www.thegpm.org/tandem ============== ========================================================== version toolchain ============== ========================================================== ``17.02.01.4`` ``GCC/6.4.0-2.28``, ``iccifort/2017.4.196-GCC-6.4.0-2.28`` ============== ========================================================== .. _list_software_xtrans_672: *xtrans* ++++++++ xtrans includes a number of routines to make X implementations transport-independent; at time of writing, it includes support for UNIX sockets, IPv4, IPv6, and DECnet. *homepage*: http://www.freedesktop.org/wiki/Software/xlibs ========= ================================================= version toolchain ========= ================================================= ``1.3.5`` ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016a`` ========= ================================================= .. _list_software_XZ_178: *XZ* ++++ xz: XZ utilities *homepage*: https://tukaani.org/xz/ ========= =================== =========================================================================================================================================================== version versionsuffix toolchain ========= =================== =========================================================================================================================================================== ``5.0.5`` ``GCC/4.8.2`` ``5.2.0`` ``GCC/4.9.2`` ``5.2.2`` ``GCC/4.9.2``, ``GCC/5.4.0-2.26``, ``GCCcore/4.9.3``, ``GCCcore/5.4.0``, ``foss/2016.04``, ``foss/2016a``, ``foss/2016b``, ``intel/2016a``, ``intel/2016b`` ``5.2.2`` ``-gettext-0.19.7`` ``foss/2016a``, ``intel/2016a`` ``5.2.3`` ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``gimkl/2017a`` ``5.2.4`` ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.2.0`` ========= =================== =========================================================================================================================================================== .. _list_software_letter_y: *Y* --- :ref:`list_software_Yade_387` - :ref:`list_software_yaff_422` - :ref:`list_software_Yambo_504` - :ref:`list_software_YAPS_317` - :ref:`list_software_Yasm_410` - :ref:`list_software_YAXT_326` .. _list_software_Yade_387: *Yade* ++++++ Yade is an extensible open-source framework for discrete numerical models, focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, allowing independent implementation of new alogrithms and interfaces. Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. *homepage*: https://yade-dem.org/doc/ ============ ================== =============================== version versionsuffix toolchain ============ ================== =============================== ``1.20.0`` ``-Python-2.7.11`` ``foss/2016a``, ``intel/2016a`` ``2016.06a`` ``-Python-2.7.12`` ``foss/2016b``, ``intel/2016b`` ``2017.01a`` ``-Python-2.7.12`` ``intel/2016b`` ``2018.02b`` ``-Python-2.7.14`` ``intel/2018a`` ============ ================== =============================== .. _list_software_yaff_422: *yaff* ++++++ Yaff stands for 'Yet another force field'. It is a pythonic force-field code. *homepage*: https://molmod.github.io/yaff/ ==================== ============================== ================================================ version versionsuffix toolchain ==================== ============================== ================================================ ``1.0.develop.2.15`` ``-Python-2.7.12-HDF5-1.8.18`` ``intel/2016b`` ``1.1.2`` ``-Python-2.7.13`` ``intel/2017a`` ``1.1.3`` ``-Python-2.7.13`` ``intel/2017a`` ``1.4.2`` ``-Python-2.7.14`` ``foss/2018a``, ``intel/2017b``, ``intel/2018a`` ``1.4.2`` ``-Python-3.6.3`` ``intel/2017b`` ``1.4.5`` ``-Python-2.7.15`` ``intel/2018b`` ``1.5.0`` ``-Python-2.7.15`` ``intel/2018b`` ``1.5.0`` ``-Python-3.7.2`` ``intel/2019a`` ``1.6.0`` ``-Python-3.7.2`` ``intel/2019a`` ``1.6.0`` ``-Python-3.7.4`` ``intel/2019b`` ==================== ============================== ================================================ .. _list_software_Yambo_504: *Yambo* +++++++ Yambo is a FORTRAN/C code for Many-Body calculations in solid state and molecular physics. Yambo relies on the Kohn-Sham wavefunctions generated by two DFT public codes: abinit, and PWscf. *homepage*: http://www.yambo-code.org ========= ========================= version toolchain ========= ========================= ``3.4.2`` ``intel/2016.02-GCC-4.9`` ========= ========================= .. _list_software_YAPS_317: *YAPS* ++++++ YAPS - Yet Another Positioning Solver *homepage*: https://github.com/baktoft/yaps ========= ============= =============== version versionsuffix toolchain ========= ============= =============== ``1.1.0`` ``-R-3.5.1`` ``foss/2018b`` ``1.1.0`` ``-R-3.6.0`` ``intel/2019a`` ========= ============= =============== .. _list_software_Yasm_410: *Yasm* ++++++ Yasm: Complete rewrite of the NASM assembler with BSD license *homepage*: http://www.tortall.net/projects/yasm/ ========= ================================================================================================================================================================================================================ version toolchain ========= ================================================================================================================================================================================================================ ``1.3.0`` ``GCCcore/6.4.0``, ``GCCcore/7.3.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``foss/2016a``, ``foss/2016b``, ``foss/2017a``, ``gimkl/2.11.5``, ``gimkl/2017a``, ``intel/2016a``, ``intel/2016b``, ``intel/2017a`` ========= ================================================================================================================================================================================================================ .. _list_software_YAXT_326: *YAXT* ++++++ Yet Another eXchange Tool *homepage*: https://www.dkrz.de/redmine/projects/yaxt ========= ================================================= version toolchain ========= ================================================= ``0.5.1`` ``intel/2016b``, ``intel/2017a``, ``intel/2017b`` ``0.6.0`` ``intel/2018a``, ``intel/2018b``, ``iomkl/2018b`` ``0.6.2`` ``iimpi/2019b`` ========= ================================================= .. _list_software_letter_z: *Z* --- :ref:`list_software_zarr_447` - :ref:`list_software_ZeroMQ_574` - :ref:`list_software_zingeR_623` - :ref:`list_software_zlib_433` - :ref:`list_software_zlibbioc_846` - :ref:`list_software_ZPAQ_316` - :ref:`list_software_zsh_341` - :ref:`list_software_zstd_453` .. _list_software_zarr_447: *zarr* ++++++ Zarr is a Python package providing an implementation of compressed, chunked, N-dimensional arrays, designed for use in parallel computing. *homepage*: http://zarr.readthedocs.io/en/stable/ ========= ================== ============== version versionsuffix toolchain ========= ================== ============== ``2.1.4`` ``-Python-2.7.13`` ``foss/2017a`` ========= ================== ============== .. _list_software_ZeroMQ_574: *ZeroMQ* ++++++++ ZeroMQ looks like an embeddable networking library but acts like a concurrency framework. It gives you sockets that carry atomic messages across various transports like in-process, inter-process, TCP, and multicast. You can connect sockets N-to-N with patterns like fanout, pub-sub, task distribution, and request-reply. It's fast enough to be the fabric for clustered products. Its asynchronous I/O model gives you scalable multicore applications, built as asynchronous message-processing tasks. It has a score of language APIs and runs on most operating systems. *homepage*: https://www.zeromq.org/ ========= ========================================================================================================= version toolchain ========= ========================================================================================================= ``4.1.4`` ``foss/2016a``, ``intel/2016a`` ``4.1.5`` ``intel/2016b`` ``4.2.0`` ``foss/2016b``, ``intel/2016b`` ``4.2.2`` ``foss/2017a``, ``foss/2017b``, ``fosscuda/2017b``, ``intel/2017a``, ``intel/2017b``, ``intelcuda/2017b`` ``4.2.5`` ``foss/2018a``, ``foss/2018b``, ``fosscuda/2018b``, ``intel/2018a``, ``intel/2018b`` ``4.3.2`` ``GCCcore/8.2.0``, ``GCCcore/8.3.0`` ========= ========================================================================================================= .. _list_software_zingeR_623: *zingeR* ++++++++ Zero-Inflated Negative binomial Gene Expression in R *homepage*: https://github.com/statOmics/zingeR ============ ============= ============== version versionsuffix toolchain ============ ============= ============== ``20180131`` ``-R-3.5.1`` ``foss/2018b`` ============ ============= ============== .. _list_software_zlib_433: *zlib* ++++++ zlib is designed to be a free, general-purpose, legally unencumbered -- that is, not covered by any patents -- lossless data-compression library for use on virtually any computer hardware and operating system. *homepage*: http://www.zlib.net/ ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== version toolchain ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== ``1.2.7`` ``GCC/4.8.1``, ``GCC/4.8.2`` ``1.2.8`` ``GCC/4.8.2``, ``GCC/4.8.3``, ``GCC/4.8.4``, ``GCC/4.9.2``, ``GCC/4.9.2-binutils-2.25``, ``GCC/4.9.3``, ``GCC/4.9.3-2.25``, ``GCC/4.9.3-binutils-2.25``, ``GCC/5.1.0-binutils-2.25``, ``GCCcore/4.9.2``, ``GCCcore/4.9.3``, ``GCCcore/4.9.4``, ``GCCcore/5.3.0``, ``GCCcore/5.4.0``, ``GCCcore/6.1.0``, ``GCCcore/6.2.0``, ``GCCcore/6.3.0``, ``GNU/4.9.3-2.25``, ``foss/2016.04``, ``foss/2016a``, ``gimkl/2.11.5``, ``intel/2016.02-GCC-4.9``, ``intel/2016a``, ``intel/2016b``, ``intel/2017.01``, ``iomkl/2016.07``, ``iomkl/2016.09-GCC-4.9.3-2.25``, ``system`` ``1.2.10`` ``system`` ``1.2.11`` ``GCCcore/5.4.0``, ``GCCcore/5.5.0``, ``GCCcore/6.3.0``, ``GCCcore/6.4.0``, ``GCCcore/7.1.0``, ``GCCcore/7.2.0``, ``GCCcore/7.3.0``, ``GCCcore/7.4.0``, ``GCCcore/8.1.0``, ``GCCcore/8.2.0``, ``GCCcore/8.3.0``, ``GCCcore/9.1.0``, ``GCCcore/9.2.0``, ``GCCcore/system``, ``gimkl/2017a``, ``system`` ========== ===================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================================== .. _list_software_zlibbioc_846: *zlibbioc* ++++++++++ This package uses the source code of zlib-1.2.5 to create libraries for systems that do not have these available via other means. *homepage*: https://bioconductor.org/packages/release/bioc/html/zlibbioc.html ========== ============= =============== version versionsuffix toolchain ========== ============= =============== ``1.18.0`` ``-R-3.2.3`` ``intel/2016a`` ``1.20.0`` ``-R-3.3.1`` ``intel/2016b`` ========== ============= =============== .. _list_software_ZPAQ_316: *ZPAQ* ++++++ zpaq is a free and open source (GPL v3) incremental, journaling command-line archiver for Windows, Linux and Mac OS/X *homepage*: http://mattmahoney.net/dc/zpaq.html ======== ============= version toolchain ======== ============= ``7.00`` ``GCC/4.8.2`` ======== ============= .. _list_software_zsh_341: *zsh* +++++ Zsh is a shell designed for interactive use, although it is also a powerful scripting language. *homepage*: http://www.zsh.org/ ========= ================== version toolchain ========= ================== ``5.1.1`` ``GNU/4.9.3-2.25`` ``5.2`` ``foss/2016b`` ========= ================== .. _list_software_zstd_453: *zstd* ++++++ Zstandard is a real-time compression algorithm, providing high compression ratios. It offers a very wide range of compression/speed trade-off, while being backed by a very fast decoder. It also offers a special mode for small data, called dictionary compression, and can create dictionaries from any sample set. *homepage*: https://facebook.github.io/zstd ========= ================================= version toolchain ========= ================================= ``1.3.4`` ``foss/2016b`` ``1.4.0`` ``GCCcore/8.2.0``, ``foss/2018b`` ========= =================================