List of supported software

EasyBuild 4.2.0 supports 1912 different software packages (incl. toolchains, bundles):

A - B - C - D - E - F - G - H - I - J - K - L - M - N - O - P - Q - R - S - T - U - V - W - X - Y - Z

3

3to2

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

4

4ti2

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

A

ABAQUS - ABINIT - ABRA2 - ABRicate - ABySS - ack - ACT - ACTC - ada - AdapterRemoval - ADDA - ADF - ADIOS - adjustText - ADMIXTURE - ADOL-C - Advisor - AFNI - AGFusion - aiohttp - ALADIN - Albacore - ALFA - alleleCount - Allinea - ALLPATHS-LG - ALPS - Amara - amask - Amber - AmberMini - AmberTools - AMD-LibM - AMD-RNG - AMD-SecureRNG - AMOS - AMPL-MP - Anaconda2 - Anaconda3 - aNCI - angsd - Annif - annovar - ANSYS - ANSYS_CFD - ant - ANTLR - ANTs - anvio - any2fasta - APBS - apex - APR - APR-util - ARAGORN - Arb - ARCH - archspec - ARGoS - argtable - Armadillo - ARPACK++ - arpack-ng - ArrayFire - Arriba - Arrow - ART - ArviZ - ARWEN - ASAP3 - ASE - ASHS - Aspera-CLI - Aspera-Connect - Assimulo - ASTRID - astropy - at-spi2-atk - at-spi2-core - ATK - ATLAS - atomate - AtomPAW - atools - ATSAS - attr - AUGUSTUS - Autoconf - Autoconf-archive - AutoDock - AutoDock_Vina - AutoGrid - Automake - autopep8 - Autotools - awscli

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

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

ABRA2

Assembly Based ReAligner

homepage: https://github.com/mozack/abra2

version	toolchain
2.22	iccifort/2019.5.281

ABRicate

Mass screening of contigs for antimicrobial and virulence genes

homepage: https://github.com/tseemann/abricate

version	versionsuffix	toolchain
0.9.9		gompi/2019b
0.9.9	-Perl-5.28.1	gompi/2019a

ABySS

Assembly By Short Sequences - a de novo, parallel, paired-end sequence assembler

homepage: https://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
2.1.5	foss/2019b

ack

ack is a tool like grep, optimized for programmers

homepage: http://beyondgrep.com/

version	toolchain
2.14	system

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

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

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

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

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

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

ADIOS

The Adaptable IO System (ADIOS) provides a simple, flexible way for scientists to describe the data in their code that may need to be written, read, or processed outside of the running simulation.

homepage: https://www.olcf.ornl.gov/center-projects/adios/

version	versionsuffix	toolchain
1.13.1	-Python-2.7.15	foss/2019a

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

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

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

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

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

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

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

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

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

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

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

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

ALLPATHS-LG

ALLPATHS-LG, the new short read genome assembler.

homepage: http://www.broadinstitute.org/software/allpaths-lg/blog/

version	toolchain
52488	foss/2016a

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

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

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

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

AmberMini

A stripped-down set of just antechamber, sqm, and tleap.

homepage: https://github.com/choderalab/ambermini

version	toolchain
16.16.0	intel/2017b

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

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

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

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

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

AMPL-MP

An open-source library for mathematical programming.

homepage: https://github.com/ampl/mp

version	toolchain
3.1.0	GCCcore/6.4.0

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

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

aNCI

Non-covalent interaction (NCI) for MD trajectories

homepage: https://www.lct.jussieu.fr/pagesperso/contrera/nci-MD.html

version	toolchain
2.0	iccifort/2019.5.281

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

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

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

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

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

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

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

ANTs

ANTs extracts information from complex datasets that include imaging. ANTs is useful for managing, interpreting and visualizing multidimensional data.

homepage: https://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
2.3.2	-Python-3.7.4	foss/2019b

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

any2fasta

Convert various sequence formats to FASTA

homepage: https://github.com/tseemann/any2fasta

version	versionsuffix	toolchain
0.4.2		GCCcore/8.3.0
0.4.2	-Perl-5.28.1	GCCcore/8.2.0

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

apex

A PyTorch Extension: Tools for easy mixed precision and distributed training in Pytorch

homepage: https://github.com/nvidia/apex

version	versionsuffix	toolchain
20200325	-Python-3.7.4	fosscuda/2019b

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

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

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

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

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

archspec

A library for detecting, labeling, and reasoning about microarchitectures

homepage: https://github.com/archspec/archspec

version	versionsuffix	toolchain
0.1.0	-Python-3.7.4	GCCcore/8.3.0

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

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, GCCcore/8.3.0, foss/2016b, foss/2018b, intel/2018a, intel/2018b

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

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

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, intel/2019b

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

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

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
0.16.0	-Python-3.7.4	intel/2019b

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

ArviZ

Exploratory analysis of Bayesian models with Python

homepage: https://github.com/arviz-devs/arviz

version	versionsuffix	toolchain
0.7.0	-Python-3.7.4	intel/2019b

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

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

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
3.19.0	-Python-3.6.6	foss/2018b, intel/2018b
3.19.0	-Python-3.7.4	foss/2019b, intel/2019b

ASHS

Automatic Segmentation of Hippocampal Subfields (ASHS)

homepage: https://sites.google.com/site/hipposubfields/home

version	toolchain
rev103_20140612	system

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

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

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

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

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

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
2.34.1	GCCcore/8.3.0

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
2.34.0	GCCcore/8.3.0

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/

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
2.34.1	GCCcore/8.3.0

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

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

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

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

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

attr

Commands for Manipulating Filesystem Extended Attributes

homepage: https://savannah.nongnu.org/projects/attr

version	toolchain
2.4.47	GCCcore/8.2.0

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
3.3.3		foss/2019b

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

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

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

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

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

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

autopep8

A tool that automatically formats Python code to conform to the PEP 8 style guide.

homepage: https://github.com/hhatto/autopep8

version	versionsuffix	toolchain
1.4.4	-Python-3.6.4	intel/2018a

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

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
1.17.7	-Python-3.7.4	GCCcore/8.3.0

B

Bader - BAGEL - bam-readcount - BAMM - BamM - BAMSurgeon - BamTools - BamUtil - Bandage - barrnap - basemap - Bash - bat - BatMeth2 - BayesAss - BayeScan - BayeScEnv - BayesTraits - Bazel - bbcp - bbFTP - BBMap - bc - BCALM - BCEL - BCFtools - bcgTree - bcl2fastq2 - bcolz - BDBag - beagle-lib - Beast - BeautifulSoup - BEDOPS - BEDTools - behave - BerkeleyGW - BFAST - BFC - bibtexparser - BiG-SCAPE - BinSanity - binutils - Bio-DB-HTS - Bio-SamTools - bioawk - biobambam2 - biomart-perl - BioPerl - Biopython - biscuit - Bismark - Bison - bitarray - BLACS - BLASR - blasr_libcpp - BLAST - BLAST+ - BLAT - Blender - BLIS - Blitz++ - BlobTools - Blosc - bmtagger - bnpy - BOINC - bokeh - BoltzTraP - Bonito - Bonmin - Bonnie++ - Boost - Boost.Python - Bottleneck - Bowtie - Bowtie2 - Bpipe - bpp-core - bpp-phyl - bpp-seq - BRAKER - BreakDancer - breseq - bsddb3 - BSMAPz - BSseeker2 - buildenv - Bullet - BUSCO - BUStools - BWA - bwa-meth - bwakit - bwidget - BWISE - bx-python - BXH_XCEDE_TOOLS - byacc - bzip2

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

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

bam-readcount

Count DNA sequence reads in BAM files

homepage: https://github.com/genome/bam-readcount

version	toolchain
0.8.0	foss/2018b

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

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

BAMSurgeon

Tools for adding mutations to existing .bam files, used for testing mutation callers

homepage: https://github.com/adamewing/bamsurgeon

version	versionsuffix	toolchain
1.2	-Python-2.7.16	GCC/8.3.0

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, GCC/8.3.0, foss/2017b, foss/2018a, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281, intel/2017b, intel/2018b

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

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

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

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

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

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

BatMeth2

An Integrated Package for Bisulfite DNA Methylation Data Analysis with Indel-sensitive Mapping.

homepage: https://github.com/GuoliangLi-HZAU/BatMeth2

version	toolchain
2.1	foss/2019b

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

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

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	GCC/8.3.0, foss/2016a, iccifort/2019.5.281

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

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

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

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

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
38.76		GCC/8.2.0-2.31.1

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

BCALM

de Bruijn graph compaction in low memory

homepage: https://github.com/GATB/bcalm

version	toolchain
2.2.0	foss/2018a

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

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
1.10.2	GCC/8.3.0

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

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

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

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

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

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

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

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

BEDTools

BEDTools: a powerful toolset for genome arithmetic. 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://bedtools.readthedocs.io/

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
2.29.2	GCC/8.3.0

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

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: https://www.berkeleygw.org

version	versionsuffix	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
2.1.0	-Python-3.7.4	foss/2019b, intel/2019b

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

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

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

BiG-SCAPE

BiG-SCAPE and CORASON provide a set of tools to explore the diversity of biosynthetic gene clusters (BGCs) across large numbers of genomes, by constructing BGC sequence similarity networks, grouping BGCs into gene cluster families, and exploring gene cluster diversity linked to enzyme phylogenies.

homepage: https://bigscape-corason.secondarymetabolites.org/index.html

version	versionsuffix	toolchain
1.0.1	-Python-3.7.4	intel/2019b

BinSanity

BinSanity contains a suite a scripts designed to cluster contigs generated from metagenomic assembly into putative genomes.

homepage: https://github.com/edgraham/BinSanity/wiki

version	versionsuffix	toolchain
0.3.5	-Python-3.7.4	foss/2019b

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
2.34	GCCcore/9.3.0, system

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

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

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

biobambam2

Tools for processing BAM files

homepage: https://github.com/gt1/biobambam2

version	toolchain
2.0.87	intel/2018a

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

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

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-2.7.16	foss/2019b
1.75	-Python-3.7.4	foss/2019b, intel/2019b

biscuit

Utilities to help analyze bisulfite-treated sequence data

homepage: https://github.com/zwdzwd/biscuit

version	toolchain
0.1.4	foss/2016a

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

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: https://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/8.2.0, GCCcore/8.3.0, GCCcore/9.1.0, GCCcore/9.2.0, system
3.5.2	system
3.5.3	GCCcore/9.3.0, system

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

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

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

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

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
2.10.0	-Linux_x86_64	system

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: https://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, iimpi/2019b

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, GCC/8.3.0, foss/2016b, foss/2018b, intel/2016b, intel/2017a

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

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

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

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

Blosc

Blosc, an extremely fast, multi-threaded, meta-compressor library

homepage: https://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
1.17.1	GCCcore/8.3.0

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

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

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

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, fosscuda/2019b

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

Bonito

Convolution Basecaller for Oxford Nanopore Reads

homepage: https://github.com/nanoporetech/bonito

version	versionsuffix	toolchain
0.1.0	-Python-3.7.4	foss/2019b, fosscuda/2019b

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

Bonnie++

Bonnie++-1.97: Enhanced performance Test of Filesystem I/O

homepage: http://www.coker.com.au/bonnie++/

version	toolchain
1.97	foss/2016a

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, gompic/2019b, iimpi/2019b

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

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

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, GCC/8.3.0, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281

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, GCC/8.3.0, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281

Bpipe

Bpipe - a tool for running and managing bioinformatics pipelines

homepage: http://docs.bpipe.org/

version	toolchain
0.9.9.2	intel/2017a

bpp-core

Bio++ Core Library

homepage: https://github.com/BioPP/bpp-core

version	toolchain
2.4.1	GCC/8.2.0-2.31.1

bpp-phyl

Bio++ Phylogenetic Library

homepage: https://github.com/BioPP/bpp-phyl

version	toolchain
2.4.1	GCC/8.2.0-2.31.1

bpp-seq

Bio++ Sequence Library

homepage: https://github.com/BioPP/bpp-seq

version	toolchain
2.4.1	GCC/8.2.0-2.31.1

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

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

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

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

BSMAPz

Updated and optimized fork of BSMAP. BSMAPz is a short reads mapping program for bisulfite sequencing in DNA methylation study.

homepage: https://github.com/zyndagj/BSMAPz

version	versionsuffix	toolchain
1.1.1	-Python-2.7.16	intel/2019b

BSseeker2

BS-Seeker2 is a seamless and versatile pipeline for accurately and fast mapping the bisulfite-treated reads.

homepage: http://pellegrini-legacy.mcdb.ucla.edu/bs_seeker2

version	versionsuffix	toolchain
2.1.8	-Python-2.7.16	GCC/8.3.0, iccifort/2019.5.281

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 <this module name>

homepage: None

version	toolchain
default	foss/2017b, foss/2018b, foss/2019b, intel/2016b, intel/2017a, intel/2019b

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

BUSCO

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

homepage: https://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
4.0.5	-Python-3.7.4	foss/2019b

BUStools

bustools is a program for manipulating BUS files for single cell RNA-Seq datasets. It can be used to error correct barcodes, collapse UMIs, produce gene count or transcript compatibility count matrices, and is useful for many other tasks. See the kallisto | bustools website for examples and instructions on how to use bustools as part of a single-cell RNA-seq workflow.

homepage: https://github.com/BUStools/bustools

version	toolchain
0.40.0	foss/2018b

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, GCC/8.3.0, foss/2017b, foss/2018a, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281, intel/2017b, intel/2018a, intel/2018b

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, iccifort/2019.5.281

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

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
1.9.14	GCCcore/8.3.0

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

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

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

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

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

C

C3D - cadaver - Caffe - cairo - cairomm - Calendrical - Cantera - canu - Canvas - CAP3 - CapnProto - Cargo - CastXML - Catch2 - CatMAP - causalml - CaVEMan - Cbc - CBLAS - ccache - CCL - cclib - CD-HIT - cDNA_Cupcake - CDO - cdsapi - CellMix - CellRanger - Centrifuge - CESM-deps - CFITSIO - cftime - CGAL - cget - Cgl - CGmapTools - CGNS - CharLS - charmm - CHARMM - CHASE - CheckM - Cheetah - CheMPS2 - Chimera - ChimPipe - Chromaprint - CIRCexplorer - CIRCexplorer2 - Circos - CIRI - cisTEM - CITE-seq-Count - Clang - Clang-Python-bindings - CLAPACK - CLHEP - CLISP - ClonalFrameML - CLooG - Clp - Clustal-Omega - ClustalW2 - Cluster-Buster - ClusterShell - CMake - CNT-ILP - CNVkit - CNVnator - CODEX2 - CoinUtils - Commet - Con3F - CONCOCT - configparser - configurable-http-proxy - ConnectomeWorkbench - Control-FREEC - CoordgenLibs - Coot - core-counter - Coreutils - corner - coverage - cowsay - CP2K - CPB - CPLEX - CppUnit - cram - cramtools - CrayCCE - CrayGNU - CrayIntel - CrayPGI - crb-blast - CRF++ - CrossMap - CrossTalkZ - CRPropa - CryptoMiniSat - CSBDeep - cscope - csvkit - ctags - ctffind - Cube - CubeGUI - CubeLib - CubeWriter - CUDA - cuDNN - Cufflinks - CUnit - cURL - custodian - cutadapt - CVS - CVXOPT - CVXPY - cysignals - Cython - cytoolz - cytosim - cyvcf2

C3D

Convert3D Medical Image Processing Tool

homepage: https://sourceforge.net/projects/c3d/

version	toolchain
1.0.0	system

cadaver

cadaver is a command-line WebDAV client for Unix.

homepage: http://www.webdav.org/cadaver/

version	toolchain
0.23.3	intel/2017a

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

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

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

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

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

canu

Canu is a fork of the Celera Assembler designed for high-noise single-molecule sequencing

homepage: https://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
1.9	-Java-11	GCCcore/8.3.0

Canvas

Copy number variant (CNV) calling from DNA sequencing data

homepage: https://github.com/Illumina/canvas

version	toolchain
1.39.0.1598	system

CAP3

CAP3 assembly program

homepage: http://seq.cs.iastate.edu/

version	toolchain
20071221-intel-x86	system
20071221-intel-x86_64	system
20071221-opteron	system

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

Cargo

The Rust package manager

homepage: https://crates.io/

version	toolchain
0.13.0	foss/2016b

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

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

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

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

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

Cbc

Cbc (Coin-or branch and cut) is an open-source mixed integer linear programming solver written in C++. It can be used as a callable library or using a stand-alone executable.

homepage: https://github.com/coin-or/Cbc

version	toolchain
2.10.3	foss/2018b

CBLAS

C interface to the BLAS

homepage: http://www.netlib.org/blas/

version	toolchain
20110120	foss/2016b

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

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

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

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

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

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

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

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

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

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

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

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

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

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, intel/2019b

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

Cgl

The COIN-OR Cut Generation Library (Cgl) is a collection of cut generators that can be used with other COIN-OR packages that make use of cuts, such as, among others, the linear solver Clp or the mixed integer linear programming solvers Cbc or BCP. Cgl uses the abstract class OsiSolverInterface (see Osi) to use or communicate with a solver. It does not directly call a solver.

homepage: https://github.com/coin-or/Cgl

version	toolchain
0.60.2	foss/2018b

CGmapTools

Command-line Toolset for Bisulfite Sequencing Data Analysis

homepage: https://cgmaptools.github.io/

version	toolchain
0.1.2	intel/2019b

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

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
2.1.0	GCCcore/8.2.0

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

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

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

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
1.1.2	-Python-3.7.4	foss/2019b, intel/2019b

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

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

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

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

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

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

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

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

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

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

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

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
10.0.0		GCCcore/8.3.0

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

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

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

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

ClonalFrameML

Efficient Inference of Recombination in Whole Bacterial Genomes

homepage: https://github.com/xavierdidelot/ClonalFrameML

version	toolchain
1.11	foss/2016b

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

Clp

Clp (Coin-or linear programming) is an open-source linear programming solver. It is primarily meant to be used as a callable library, but a basic, stand-alone executable version is also available.

homepage: https://github.com/coin-or/Clp

version	toolchain
1.17.3	foss/2018b

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	GCC/8.3.0, foss/2018b, intel/2018a, intel/2018b

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

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

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

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

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

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

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

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

CoinUtils

CoinUtils (Coin-OR Utilities) is an open-source collection of classes and functions that are generally useful to more than one COIN-OR project.

homepage: https://github.com/coin-or/CoinUtils

version	toolchain
2.11.3	GCCcore/7.3.0

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

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

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

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

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

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

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

CoordgenLibs

Schrodinger-developed 2D Coordinate Generation

homepage: https://github.com/schrodinger/coordgenlibs

version	toolchain
1.3.2	gompi/2019a, iimpi/2019a

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

core-counter

Tool to check available cores and OMP threads

homepage: https://github.com/gjbex/core-counter

version	toolchain
1.1.1	system

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

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

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

cowsay

Configurable talking characters in ASCII art

homepage: https://github.com/tnalpgge/rank-amateur-cowsay

version	toolchain
3.04	system

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

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

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

CppUnit

CppUnit is the C++ port of the famous JUnit framework for unit testing.

homepage: https://freedesktop.org/wiki/Software/cppunit/

version	toolchain
1.12.1	GCCcore/6.4.0, GCCcore/7.3.0, foss/2016a
1.15.1	GCCcore/8.3.0

cram

Cram is a functional testing framework for command line applications.

homepage: https://bitheap.org/cram

version	toolchain
0.7	GCCcore/8.2.0

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

CrayCCE

Toolchain using Cray compiler wrapper, using PrgEnv-cray (PE release: June 2019).

homepage: https://pubs.cray.com/discover

version	toolchain
19.06	system

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

CrayIntel

Toolchain using Cray compiler wrapper, using PrgEnv-intel (PE release: June 2019).

homepage: https://pubs.cray.com/discover

version	toolchain
19.06	system

CrayPGI

Toolchain using Cray compiler wrapper, PrgEnv-pgi compiler (PE release: June 2019).

homepage: https://pubs.cray.com/discover

version	toolchain
19.06	system

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	versionsuffix	toolchain
0.6.9		intel/2017a
0.6.9	-Ruby-2.6.1	foss/2018b

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

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

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

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

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

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

cscope

Cscope is a developer’s tool for browsing source code.

homepage: http://cscope.sourceforge.net/

version	toolchain
15.9	system

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

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

ctffind

Program for finding CTFs of electron micrographs.

homepage: https://grigoriefflab.umassmed.edu/ctffind4

version	toolchain
4.1.13	foss/2019a, fosscuda/2019a

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

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

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

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

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

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

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

CUnit

Automated testing framework for C.

homepage: https://sourceforge.net/projects/cunit/

version	toolchain
2.1-3	GCCcore/6.4.0

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

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

cutadapt

Cutadapt finds and removes adapter sequences, primers, poly-A tails and other types of unwanted sequence from your high-throughput sequencing reads.

homepage: https://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, GCCcore/8.3.0
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
2.7	-Python-3.7.4	GCCcore/8.3.0
2.8	-Python-3.7.4	GCCcore/8.3.0

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

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

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	versionsuffix	toolchain
1.0.24		foss/2019a
1.0.28	-Python-3.7.4	foss/2019b

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

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

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

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

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

D

dadi - dagitty - damageproto - dammit - DANPOS2 - DAS_Tool - dask - datamash - davix - DB - DB_File - DBD-mysql - DBG2OLC - DBus - dbus-glib - dcm2niix - DCMTK - deal.II - deap - deconf - DeconICA - deepdiff - DeepSurv - deepTools - Delly - DeMixT - DendroPy - destiny - detonate - DFT-D3 - DFTB+ - DIAL - DIAMOND - DicomBrowser - Diffutils - dill - distributed - DL_POLY_Classic - DMTCP - DOLFIN - Doris - dotNET-Core-Runtime - double-conversion - Doxygen - Drake - dropEst - DSA - DSRC - Dsuite - dtcmp - dtcwt - dxpy

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

dagitty

A port of the web-based software ‘DAGitty’, available at <http://dagitty.net>, 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

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

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

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

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

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, fosscuda/2019b

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

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: https://dmc.web.cern.ch/projects/davix/home

version	toolchain
0.6.6	intel/2017a
0.7.5	GCCcore/8.3.0

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, GCCcore/8.3.0

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

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

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

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

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

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, GCCcore/8.2.0

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

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

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

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

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

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

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

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

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

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

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, GCCcore/8.3.0, intel/2019a
4.4.0	-Python-2.7.15	intel/2018b

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

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

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	GCC/8.3.0, intel/2019a

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

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

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
0.9.30	GCC/8.3.0, iccifort/2019.5.281

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

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

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

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

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

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

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

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

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

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

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

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

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

DSA

Digital Sorting Algorithm

homepage: https://github.com/zhandong/DSA

version	versionsuffix	toolchain
1.0	-R-3.5.1	foss/2018b

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

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

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

dtcwt

Dual-Tree Complex Wavelet Transform library for Python

homepage: https://github.com/rjw57/dtcwt

version	versionsuffix	toolchain
0.12.0	-Python-2.7.15	foss/2018b
0.12.0	-Python-3.7.4	intel/2019b

dxpy

DNAnexus Platform API bindings for Python

homepage: http://autodoc.dnanexus.com/

version	versionsuffix	toolchain
0.266.1	-Python-2.7.14	intel/2018a

E

ea-utils - earthengine-api - EasyBuild - EasyQC - ecCodes - ED2 - EggLib - eggnog-mapper - Eigen - EIGENSOFT - elastix - Elk - ELPA - ELPH - ELSI - Emacs - EMAN2 - EMBOSS - emcee - enaBrowserTool - enchant - EnsEMBLCoreAPI - entrypoints - EPD - EPIC - EricScript - ESMF - Essentia - ETE - ETSF_IO - eudev - EvidentialGene - evmix - ExaBayes - Exonerate - expat - expect - eXpress - Extrae

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

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

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
4.1.1	system
4.1.2	system

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

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

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

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

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

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

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

elastix

elastix: a toolbox for rigid and nonrigid registration of images.

homepage: http://elastix.isi.uu.nl/

version	toolchain
4.9.0	foss/2018a

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

ELPA

Eigenvalue SoLvers for Petaflop-Applications .

homepage: https://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
2019.11.001	foss/2019b, intel/2019b

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

ELSI

ELSI provides and enhances scalable, open-source software library solutions for electronic structure calculations in materials science, condensed matter physics, chemistry, and many other fields. ELSI focuses on methods that solve or circumvent eigenvalue problems in electronic structure theory. The ELSI infrastructure should also be useful for other challenging eigenvalue problems.

homepage: https://wordpress.elsi-interchange.org/

version	versionsuffix	toolchain
2.5.0		intel/2019b
2.5.0	-PEXSI	intel/2019b

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

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

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	-Java-11	GCC/8.3.0
6.6.0	-X11-20170314	intel/2017a

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

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

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

EnsEMBLCoreAPI

The Ensembl Core Perl API and SQL schema

homepage: https://www.ensembl.org/info/docs/api/index.html

version	versionsuffix	toolchain
96.0-r20190601	-Perl-5.28.1	foss/2019a

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

eXpress

Streaming quantification for high-throughput sequencing

homepage: https://pachterlab.github.io/eXpress

version	toolchain
1.5.1	intel/2017b

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

F

f90cache - Faber - faceswap - FALCON - FANN - fast5 - FASTA - FastaIndex - FastANI - FastME - fastp - fastPHASE - fastq-pair - fastq-tools - FastQ_Screen - FastQC - FastQTL - fastqz - FastRFS - fastStructure - FastTree - FASTX-Toolkit - fatslim - fbm - FCM - FDS - fdstools - FDTD_Solutions - feh - Ferret - FFC - FFLAS-FFPACK - FFmpeg - ffnet - FFTW - FGSL - FIAT - FigureGen - Fiji - file - Filtlong - find_circ - findhap - findutils - fineRADstructure - fineSTRUCTURE - Fiona - Firefox - FireWorks - fixesproto - FLANN - FLASH - Flask - FLEUR - flex - FlexiDot - FLINT - FLTK - FLUENT - Flye - FMILibrary - FMRIprep - fmt - FoldX - fontconfig - fontsproto - foss - fosscuda - FoX - FPM - fqtrim - fqzcomp - FragGeneScan - FRANz - FreeFem++ - freeglut - FreeImage - FreeSurfer - freetype - FreeXL - FriBidi - FSL - FSLeyes - FTGL - fullrmc - FUNWAVE-TVD - FUSE - FuSeq - future - fxtract

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

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

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

FALCON

Falcon: a set of tools for fast aligning long reads for consensus and assembly

homepage: https://github.com/PacificBiosciences/FALCON

version	versionsuffix	toolchain
1.8.8		intel/2017b
1.8.8	-Python-2.7.16	intel/2019b

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

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

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

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

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
1.3	iccifort/2019.5.281

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	GCC/8.3.0, iccifort/2019.5.281, intel/2018a, intel/2018b

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, GCC/8.3.0, iccifort/2019.5.281

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

fastq-pair

Match up paired end fastq files quickly and efficiently.

homepage: https://github.com/linsalrob/fastq-pair

version	toolchain
1.0	GCCcore/8.2.0

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

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

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
0.11.9	-Java-11	system

FastQTL

FastQTL is a QTL mapper

homepage: http://fastqtl.sourceforge.net/

version	toolchain
2.184	foss/2018b

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

FastRFS

Fast Robinson Foulds Supertrees

homepage: https://github.com/pranjalv123/FastRFS

version	toolchain
1.0-20190613	gompi/2019a

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

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, GCCcore/8.3.0

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

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

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

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

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

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

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

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

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: https://ferret.pmel.noaa.gov/Ferret/

version	toolchain
7.3	intel/2017b
7.5.0	foss/2019b

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

FFLAS-FFPACK

Finite Field Linear Algebra Subroutines / Package

homepage: https://linbox-team.github.io/fflas-ffpack/

version	toolchain
2.2.0	foss/2016a

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

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

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

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

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

FigureGen

FigureGen is a Fortran program that creates images for ADCIRC files. It reads mesh files (fort.14, etc.), nodal attributes files (fort.13, etc.) and output files (fort.63, fort.64, maxele.63, etc.). It plots contours, contour lines, and vectors. Using FigureGen, you can go directly from the ADCIRC input and output files to a presentation-quality figure, for one or multiple time snaps.

homepage: https://ccht.ccee.ncsu.edu/category/software/figuregen/

version	toolchain
51-20190516	foss/2019a

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

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

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

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

findhap

Find haplotypes and impute genotypes using multiple chip sets and sequence data

homepage: http://aipl.arsusda.gov/software/findhap/

version	toolchain
4	system

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

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

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

Fiona

Fiona is designed to be simple and dependable. It focuses on reading and writing data in standard Python IO style and relies upon familiar Python types and protocols such as files, dictionaries, mappings, and iterators instead of classes specific to OGR. Fiona can read and write real-world data using multi-layered GIS formats and zipped virtual file systems and integrates readily with other Python GIS packages such as pyproj, Rtree, and Shapely.

homepage: https://github.com/Toblerity/Fiona

version	versionsuffix	toolchain
1.8.13	-Python-3.7.4	foss/2019b

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

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

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

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

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

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

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

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, GCCcore/8.3.0, 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/9.3.0, GCCcore/system, system

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

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

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

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

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
2.6	-Python-3.7.4	intel/2019b

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, GCCcore/8.3.0

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

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

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

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

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

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

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

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

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

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

FuSeq

FuSeq is a novel method to discover fusion genes from paired-end RNA sequencing data.

homepage: https://github.com/nghiavtr/FuSeq

version	toolchain
1.1.2	gompi/2019b

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

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

G

g2clib - g2lib - g2log - Gaia - GAMESS-US - gap - GapCloser - GapFiller - GARLI - GAT - GATE - GATK - Gblocks - gbs2ploidy - gc - GC3Pie - GCC - GCCcore - gcccuda - GConf - Gctf - GD - GDAL - GDB - gdbgui - gdc-client - GDCHART - GDCM - GDGraph - gdist - Gdk-Pixbuf - Geant4 - gearshifft - GEM-library - GEMMA - gencore_variant_detection - GeneMark-ET - GenomeMapper - GenomeTester4 - GenomeThreader - GenomeTools - GenotypeHarmonizer - gensim - geopy - GEOS - Gerris - GETORB - gettext - GffCompare - gffread - gflags - GFOLD - GHC - Ghostscript - giflib - gifsicle - GIMIC - gimkl - gimpi - gimpic - GIMPS - giolf - giolfc - git - git-lfs - GitPython - Givaro - Giza - GL2PS - Glade - glew - GLib - glibc - GLibmm - GLIMMER - GlimmerHMM - GLM - GlobalArrays - Globus-CLI - GlobusConnectPersonal - glog - GLPK - glproto - GMAP-GSNAP - GMP - gmpich - gmpolf - gmpy2 - gmsh - GMT - gmvapich2 - gmvolf - GNU - gnuplot - GnuTLS - Go - GObject-Introspection - golf - gomkl - gompi - gompic - google-java-format - googletest - GP2C - GPAW - GPAW-setups - gperf - gperftools - gpustat - Grace - grace - Gradle - gradunwarp - graph-tool - Graphene - GraphicsMagick - GraphMap2 - Graphviz - graphviz - GRASP - GRASS - Greenlet - Grep - grib_api - GRIT - GRNBoost - GroIMP - GROMACS - GromacsWrapper - GroopM - Groovy - gsettings-desktop-schemas - GSL - gSOAP - gsport - GST-plugins-base - GStreamer - GTDB-Tk - gtest - GTK+ - GtkSourceView - GTOOL - GTS - gubbins - guenomu - Guile - GULP - Gurobi - gzip

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

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

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	GCCcore/8.3.0, foss/2016b

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

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

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

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

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

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

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

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

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
4.1.4.1	-Java-11	GCCcore/8.3.0

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

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

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

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

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		system
9.2.0	-2.32	system
system		system
system	-2.29	system

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
9.3.0	system
system	system

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

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

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

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

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	foss/2019b, intel/2019b

GDB

The GNU Project Debugger

homepage: https://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
9.1	-Python-3.7.4	GCCcore/8.3.0

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

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

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

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

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

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

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
2.38.2	GCCcore/8.3.0

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

gearshifft

Benchmark Suite for Heterogenuous FFT Implementations

homepage: https://github.com/mpicbg-scicomp/gearshifft

version	toolchain
0.4.0	foss/2019a

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

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

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

GeneMark-ET

Eukaryotic gene prediction suite with automatic training

homepage: http://exon.gatech.edu/GeneMark

version	toolchain
4.38	GCCcore/8.2.0

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

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

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

GenomeTools

A comprehensive software library for efficient processing of structured genome annotations.

homepage: http://genometools.org

version	versionsuffix	toolchain
1.5.10		foss/2018b
1.5.10	-Python-2.7.15	foss/2018b
1.6.1		GCC/8.3.0
1.6.1	-Python-2.7.16	GCC/8.3.0

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

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

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

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	GCC/8.3.0, iccifort/2019.5.281

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

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

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

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

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

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

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

GHC

The Glorious/Glasgow Haskell Compiler

homepage: http://haskell.org/ghc/

version	toolchain
6.12.3	system

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

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

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

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

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

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

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

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

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

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

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

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

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

Givaro

C++ library for arithmetic and algebraic computations

homepage: http://givaro.forge.imag.fr/

version	toolchain
4.0.1	foss/2016a

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

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		GCCcore/8.3.0, foss/2017b, foss/2018a, foss/2018b, foss/2019a, intel/2017a, intel/2017b, intel/2018a

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

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

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

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

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

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

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

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

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

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

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

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

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, GCCcore/8.3.0

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

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
2019-09-12	GCC/8.3.0

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

gmpich

gcc and GFortran based compiler toolchain, including MPICH for MPI support.

homepage: (none)

version	toolchain
2016a	system
2017.08	system

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

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

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

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

gmvapich2

GNU Compiler Collection (GCC) based compiler toolchain, including MVAPICH2 for MPI support.

homepage: (none)

version	toolchain
1.7.20	system
2016a	system

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

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

gnuplot

Portable interactive, function plotting utility

homepage: https://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
5.2.8	GCCcore/8.3.0

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

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
1.14	system
1.14.1	system

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
1.58.3	-Python-2.7.16	GCCcore/8.3.0
1.60.1	-Python-3.7.2	GCCcore/8.2.0
1.63.1	-Python-3.7.4	GCCcore/8.3.0

golf

GNU Compiler Collection (GCC) based compiler toolchain, including OpenBLAS (BLAS and LAPACK support) and FFTW.

homepage: (none)

version	toolchain
2018a	system

gomkl

GNU Compiler Collection (GCC) based compiler toolchain with OpenMPI and MKL

homepage: (none)

version	toolchain
2018b	system
2019a	system

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

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

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

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

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

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
20.1.0	-Python-3.7.4	foss/2019b, intel/2019b

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

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

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: https://github.com/gperftools/gperftools

version	toolchain
2.5	foss/2016a, intel/2016b
2.6.3	GCCcore/6.4.0
2.7.90	GCCcore/8.3.0

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

Grace

Grace is a WYSIWYG tool to make two-dimensional plots of numerical data.

homepage: https://plasma-gate.weizmann.ac.il/Grace/

version	versionsuffix	toolchain
5.1.25	-5build1	foss/2017b, foss/2018a, foss/2019a, foss/2019b, intel/2017b, intel/2019a, intel/2019b

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

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
6.1.1	system

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

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

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

GraphicsMagick

GraphicsMagick is the swiss army knife of image processing.

homepage: https://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
1.3.34	foss/2019a, foss/2019b

GraphMap2

A highly sensitive and accurate mapper for long, error-prone reads

homepage: https://github.com/lbcb-sci/graphmap2

version	toolchain
0.6.4	foss/2019b

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: https://www.graphviz.org/

version	versionsuffix	toolchain
2.38.0		foss/2016b, intel/2016b
2.40.1		foss/2018b, intel/2018a
2.40.1	-Python-2.7.15	foss/2018b
2.42.2		foss/2019b
2.42.2	-Python-3.7.4	foss/2019b

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

GRASP

The General Relativistic Atomic Structure Package (GRASP) is a set of Fortran 90 programs for performing fully-relativistic electron structure calculations of atoms.

homepage: https://compas.github.io/grasp/

version	toolchain
2018	foss/2019b

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

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

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

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

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

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

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

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
2020		foss/2019b, fosscuda/2019b

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

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

Groovy

Groovy is a powerful, optionally typed and dynamic language, with static-typing and static compilation capabilities, for the Java platform aimed at improving developer productivity thanks to a concise, familiar and easy to learn syntax.

homepage: https://groovy-lang.org

version	versionsuffix	toolchain
2.5.9	-Java-11	system

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

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

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
2.8.100	GCCcore/8.3.0

gsport

GSPORT command-line tool for accessing GenomeScan Customer Portal

homepage: https://github.com/genomescan/gsport

version	versionsuffix	toolchain
1.4.2	-Python-3.7.4	GCCcore/8.3.0

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

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

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
1.0.2	-Python-3.7.4	intel/2019b

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
1.10.0	GCCcore/8.3.0

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
3.24.13	GCCcore/8.3.0

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

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

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

gubbins

Gubbins (Genealogies Unbiased By recomBinations In Nucleotide Sequences) is an algorithm that iteratively identifies loci containing elevated densities of base substitutions while concurrently constructing a phylogeny based on the putative point mutations outside of these regions. Simulations demonstrate the algorithm generates highly accurate reconstructions under realistic models of short-term bacterial evolution, and can be run in only a few hours on alignments of hundreds of bacterial genome sequences.

homepage: https://sanger-pathogens.github.io/gubbins

version	toolchain
2.4.0	system

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

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

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

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
9.0.0	-Python-3.7.4	GCCcore/8.3.0
9.0.1		system

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, GCCcore/8.3.0

H

h4toh5 - H5hut - h5py - Hadoop - hanythingondemand - HAPGEN2 - HarfBuzz - Harminv - HBase - HDDM - HDF - HDF5 - hdf5storage - HDFView - HEALPix - heaptrack - Hello - help2man - HH-suite - HiC-Pro - HiCExplorer - HIPS - HISAT2 - HLAminer - HMMER - hmmlearn - HOME - Horovod - horton - HPCG - HPCX - HPDBSCAN - HPL - htop - HTSeq - HTSlib - hub - hunspell - hwloc - Hyperopt - hyperspy - HyPhy - hypothesis - Hypre

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

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

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

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

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

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

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
2.6.4	GCCcore/8.3.0

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

HBase

Apache HBase. is the Hadoop database, a distributed, scalable, big data store.

homepage: http://hbase.apache.org/

version	toolchain
1.0.2	system

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
0.7.5	-Python-2.7.16	intel/2019b

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

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

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

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

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

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

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

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
1.47.12	GCCcore/9.3.0

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

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

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

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

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

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

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

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

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

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-1.15.2-Python-3.7.4	fosscuda/2019b
0.18.2	-TensorFlow-2.0.0-Python-3.7.4	fosscuda/2019b
0.19.1	-TensorFlow-2.1.0-Python-3.7.4	fosscuda/2019b

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

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

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

HPDBSCAN

Highly parallel density based spatial clustering for application with noise

homepage: https://bitbucket.org/markus.goetz/hpdbscan

version	toolchain
20171110	foss/2017b

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

htop

An interactive process viewer for Unix

homepage: http://hisham.hm/htop/

version	toolchain
2.0.0	system
2.0.1	system

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

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
1.10.2		GCC/8.3.0, iccifort/2019.5.281
20160107	-PacBio	intel/2017a

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

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

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

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

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

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

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

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
2.18.2	foss/2019b, intel/2019b

I

i-cisTarget - i-PI - I-TASSER - ICA-AROMA - icc - iccifort - iccifortcuda - icmake - iCount - ICU - IDBA-UD - ieeg-cli - ifort - IGMPlot - igraph - IGV - igv-reports - IGVTools - iimpi - iimpic - IMa2 - IMa2p - imageio - ImageJ - ImageMagick - imake - IMB - imbalanced-learn - imgaug - imkl - Imlib2 - IMOD - impi - IMPUTE2 - Inelastica - inferCNV - Infernal - Infomap - inputproto - Inspector - IntaRNA - INTEGRATE - INTEGRATE-Neo - intel - IntelClusterChecker - intelcuda - IntelPython - InterProScan - intltool - io_lib - iomkl - iompi - IOR - IOzone - Ipopt - ipp - IPy - ipyparallel - ipyrad - IPython - IQ-TREE - IRkernel - IronPython - ISL - ispc - itac - ITK - ITSTool - iVar

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

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

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

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

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

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
2020.0.166	-GCC-9.2.0	system
system	-GCC-system-2.29	system

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

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

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

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

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

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

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

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

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: https://igraph.org

version	toolchain
0.7.1	foss/2018b, intel/2016b, intel/2017b
0.8.0	foss/2019b

IGV

This package contains command line utilities for preprocessing, computing feature count density (coverage), sorting, and indexing data files.

homepage: https://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
2.8.0	-Java-11	system

igv-reports

Python application to generate self-contained igv.js pages that can be opened within a browser with “file” protocol.

homepage: https://github.com/igvteam/igv-reports

version	versionsuffix	toolchain
0.9.8	-Python-3.7.4	GCC/8.3.0

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

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

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

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

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

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

ImageJ

Image Processing and Analysis in Java

homepage: https://imagej.nih.gov/ij

version	toolchain
1.51a	system
1.51i	system
1.51k	system

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

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

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

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

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

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

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

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

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-GCC-9.2.0
system		iccifort/system-GCC-system-2.29

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

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

inferCNV

InferCNV is used to explore tumor single cell RNA-Seq data to identify evidence for somatic large-scale chromosomal copy number alterations, such as gains or deletions of entire chromosomes or large segments of chromosomes.

homepage: https://github.com/broadinstitute/inferCNV/wiki

version	versionsuffix	toolchain
1.0.4	-Python-3.7.2-R-3.6.0	foss/2019a

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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, fosscuda/2019b, intel/2019b

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
1.6.12		intel/2019b

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
1.1	-R-3.6.2-Python-3.7.4	foss/2019b, fosscuda/2019b

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

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

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
1.12.0	system

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

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
5.0.1	-Python-3.7.4	foss/2019b
5.0b01	-Python-3.6.6	foss/2018b

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

iVar

iVar is a computational package that contains functions broadly useful for viral amplicon-based sequencing.

homepage: https://github.com/andersen-lab/ivar

version	toolchain
1.0.1	foss/2018b

J

JAGS - Jansson - JasPer - Java - JAXFrontCE - jbigkit - Jellyfish - jemalloc - jhbuild - JiTCODE - jModelTest - joypy - jq - JsonCpp - JUBE - Judy - Julia - JUnit - jupyterhub - JupyterLab - JWM

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, foss/2019a, intel/2017b

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

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

Java

Java Platform, Standard Edition (Java SE) lets you develop and deploy Java applications on desktops and servers.

homepage: https://java.com/

version	versionsuffix	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
1.8.0_241		system
1.8_191-b26-OpenJDK		system
1.9.0.4		system
11		system
11.0.2		system
11.0.6	-ppc64le	system
13		system
13.0.2		system

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

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

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, GCC/8.3.0

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

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

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

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

joypy

Joyplots in Python with matplotlib & pandas

homepage: https://github.com/sbebo/joypy

version	versionsuffix	toolchain
0.2.2	-Python-3.7.4	intel/2019b

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

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

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

Judy

A C library that implements a dynamic array.

homepage: http://judy.sourceforge.net/

version	toolchain
1.0.5	GCCcore/8.2.0

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
1.4.0	-linux-x86_64	system

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

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

JupyterLab

JupyterLab is the next-generation user interface for Project Jupyter offering all the familiar building blocks of the classic Jupyter Notebook (notebook, terminal, text editor, file browser, rich outputs, etc.) in a flexible and powerful user interface. JupyterLab will eventually replace the classic Jupyter Notebook.

homepage: https://jupyter.org/

version	versionsuffix	toolchain
1.2.5	-Python-3.7.4	foss/2019b, fosscuda/2019b

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

K

Kaiju - kallisto - KAT - kbproto - Kent_tools - Keras - khmer - kim-api - kma - KMC - KmerGenie - KNIME - kpcalg - Kraken - Kraken2 - Kratos - KronaTools - kwant - KWIML - kWIP - KyotoCabinet

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
1.7.3	-Python-3.7.4	gompi/2019b

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: https://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
0.46.1	foss/2019b

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

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

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

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
2.3.1	-Python-3.7.4	foss/2019b, fosscuda/2019b

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

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
2.1.3	foss/2019b, intel/2019b

kma

KMA is a mapping method designed to map raw reads directly against redundant databases, in an ultra-fast manner using seed and extend.

homepage: https://bitbucket.org/genomicepidemiology/kma

version	toolchain
1.2.22	intel/2019b

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

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

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

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

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

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
2.0.8-beta	-Perl-5.30.0	gompi/2019b

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

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

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

KWIML

The Kitware Information Macro Library

homepage: https://gitlab.kitware.com/utils/kwiml

version	toolchain
20180201	GCCcore/6.4.0

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

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

L

L_RNA_scaffolder - LAME - LAMMPS - lancet - LAST - LASTZ - lavaan - LCov - LeadIT - LEMON - Leptonica - less - LevelDB - lftp - libaio - libarchive - libBigWig - libbitmask - libcerf - libcircle - libcmaes - libconfig - libcpuset - libcroco - libctl - libdap - libdrm - libdwarf - libedit - libelf - libepoxy - libevent - libffcall - libffi - libFLAME - libfontenc - libgcrypt - libgd - libgeotiff - libglade - libGLU - libglvnd - libgpg-error - libgpuarray - libGridXC - libgtextutils - libharu - libibmad - libibumad - libICE - libiconv - libidn - Libint - libjpeg-turbo - libmatheval - libmaus2 - libMemcached - libpciaccess - libpng - libpsl - libpsml - libPSML - libpsortb - libpthread-stubs - libQGLViewer - libreadline - libRmath - librsvg - libsamplerate - libsigc++ - libsigsegv - libSM - libsndfile - libsodium - LibSoup - libspatialindex - libspatialite - libssh - LIBSVM - libtar - libtasn1 - LibTIFF - libtirpc - libtool - libunistring - libunwind - libutempter - LibUUID - libvdwxc - libwebp - libX11 - libXau - libxc - libxcb - libXcursor - libXdamage - libXdmcp - libXext - libXfixes - libXfont - libXft - libXi - libXinerama - libxkbcommon - libxml++ - libxml2 - libxml2-python - libXmu - libXp - libXpm - libXrandr - libXrender - libxslt - libxsmm - libXt - libXxf86vm - libyaml - libzip - lifelines - Lighter - likwid - LinBox - LittleCMS - LLVM - LMDB - LMfit - Lmod - LocARNA - LoFreq - Log-Log4perl - LOHHLA - Loki - Longshot - lpsolve - lrslib - LS-PrePost - LSMS - LtrDetector - Lua - LuaJIT - Lucene-Geo-Gazetteer - LUMPY - LUSCUS - lwgrp - lxml - lynx - lz4 - LZO

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

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

LAMMPS

LAMMPS is a classical molecular dynamics code, and an acronym for Large-scale Atomic/Molecular Massively Parallel Simulator. LAMMPS has potentials for solid-state materials (metals, semiconductors) and soft matter (biomolecules, polymers) and coarse-grained or mesoscopic systems. It can be used to model atoms or, more generically, as a parallel particle simulator at the atomic, meso, or continuum scale. LAMMPS runs on single processors or in parallel using message-passing techniques and a spatial-decomposition of the simulation domain. The code is designed to be easy to modify or extend with new functionality.

homepage: https://lammps.sandia.gov/

version	versionsuffix	toolchain
3Mar2020	-Python-3.7.4-kokkos	foss/2019b, intel/2019b
7Aug2019	-Python-3.7.4-kokkos	foss/2019b, intel/2019b

lancet

Lancet is a somatic variant caller (SNVs and indels) for short read data.

homepage: https://github.com/nygenome/lancet

version	toolchain
1.1.0	iccifort/2019.5.281

LAST

LAST finds similar regions between sequences.

homepage: http://last.cbrc.jp/

version	toolchain
869	intel/2017a
914	intel/2017b
1045	intel/2019b

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: https://www.bx.psu.edu/~rsharris/lastz/

version	toolchain
1.02.00	foss/2016a
1.04.03	foss/2019b

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

LCov

LCOV - the LTP GCOV extension

homepage: http://ltp.sourceforge.net/coverage/lcov.php

version	toolchain
1.13	GCCcore/7.2.0

LeadIT

Visually Informed LeadOpt

homepage: http://www.biosolveit.de/LeadIT/index.html

version	toolchain
2.1.9	system

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

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

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

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

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

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

libarchive

Multi-format archive and compression library

homepage: https://www.libarchive.org/

version	toolchain
3.4.0	GCCcore/8.2.0

libBigWig

A C library for handling bigWig files

homepage: https://github.com/dpryan79/libBigWig

version	toolchain
0.4.4	GCCcore/8.3.0

libbitmask

libbitmask provides a convenient, powerful bitmask data type

homepage: http://oss.sgi.com/projects/cpusets/

version	toolchain
2.0	system

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

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

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

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

libcpuset

libcpuset provides full access to cpuset capabilities

homepage: http://oss.sgi.com/projects/cpusets/

version	toolchain
1.0	system

libcroco

Libcroco is a standalone css2 parsing and manipulation library.

homepage: https://github.com/GNOME/libcroco

version	toolchain
0.6.11	intel/2016a

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

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

libdrm

Direct Rendering Manager runtime library.

homepage: https://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

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

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

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

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
1.5.4	GCCcore/8.3.0

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/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0, system
2.1.11	GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.3.0

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

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

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

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

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

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

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

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

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

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

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

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
0.7.6	-Python-3.7.4	fosscuda/2019b

libGridXC

A library to compute the exchange and correlation energy and potential in spherical (i.e. an atom) or periodic systems. It is based on SiestaXC.

homepage: https://launchpad.net/libgridxc

version	toolchain
0.8.5	iimpi/2019b

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

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, GCCcore/8.3.0, foss/2016a, foss/2016b, intel/2017a, intel/2018b

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

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

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

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

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, GCCcore/8.3.0

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

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

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

libmaus2

libmaus2 is a collection of data structures and algorithms.

homepage: https://github.com/gt1/libmaus2

version	toolchain
2.0.453	intel/2018a

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

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

libpng

libpng is the official PNG reference library

homepage: http://www.libpng.org/pub/png/libpng.html

version	toolchain
1.2.58	system
1.2.59	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

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

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

libPSML

A library to handle PSML, the pseudopotential markup language.

homepage: https://launchpad.net/libpsml

version	toolchain
1.1.8	iccifort/2019.5.281

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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: https://www.csie.ntu.edu.tw/~cjlin/libsvm/

version	toolchain
3.22	intel/2016b, intel/2017b
3.23	foss/2018b, intel/2018b

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

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

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

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

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

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

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

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

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

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: https://libvdwxc.org

version	toolchain
0.3.2	foss/2018b
0.4.0	foss/2019a, foss/2019b

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

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

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

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, GCC/8.3.0, iccifort/2019.1.144-GCC-8.2.0-2.31.1, iccifort/2019.5.281

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

libXcursor

X Cursor management library

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.1.14	foss/2016a, intel/2016a

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

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

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

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

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

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

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

libXinerama

Xinerama multiple monitor library

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.1.3	foss/2016a, intel/2016a

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

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

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

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

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

libXp

libXp provides the X print library.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.0.3	intel/2016a

libXpm

libXp provides the X print library.

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
3.5.11	foss/2016a, intel/2016a

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

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

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

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

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

libXxf86vm

X11 XFree86 video mode extension library

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.1.4	foss/2016a, intel/2016a

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

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

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

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

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
5.0.1	GCCcore/8.3.0

LinBox

C++ library for exact, high-performance linear algebra

homepage: http://linalg.org/

version	toolchain
1.4.0	foss/2016a

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

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: https://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
8.0.1	GCCcore/8.3.0
9.0.0	GCCcore/8.3.0
9.0.1	GCCcore/8.3.0
10.0.0	GCCcore/8.3.0

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

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
0.9.14	-Python-2.7.15	intel/2018b

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

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

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

Log-Log4perl

Log4perl

homepage: https://metacpan.org/pod/Log::Log4perl

version	toolchain
1.47	foss/2016a

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

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

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

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

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

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
4.7.8		system

LSMS

LSMS benchmark, part of CORAL suite

homepage: https://asc.llnl.gov/CORAL-benchmarks/#lsms

version	toolchain
3_rev237	foss/2016a

LtrDetector

A modern tool-suite for detectinglong terminal repeat retrotransposons de-novo onthe genomic scale

homepage: https://github.com/TulsaBioinformaticsToolsmith/LtrDetector

version	versionsuffix	toolchain
1.0	-Python-3.7.4	intel/2019b

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, GCCcore/8.3.0
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, GCCcore/8.3.0, system

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

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

LUMPY

A probabilistic framework for structural variant discovery.

homepage: https://github.com/arq5x/lumpy-sv

version	toolchain
0.2.13	foss/2016b

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

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

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

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

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

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, GCCcore/8.3.0, foss/2016a, foss/2016b, foss/2017a, foss/2018a, foss/2018b, fosscuda/2018b, intel/2017a

M

M4 - MACH - MACS2 - maeparser - MAFFT - magick - magma - MAGMA - MagresPython - mahotas - MAJIQ - make - makedepend - makedepf90 - Mako - manta - Maple - MapSplice - Maq - MariaDB - MariaDB-connector-c - Mash - MaSuRCA - Mathematica - MathGL - MATIO - MATLAB - MATLAB-Engine - matplotlib - MATSim - Maven - mawk - MaxBin - MaxQuant - mayavi - mc - MCL - MCR - MDBM - MDSplus - mdtest - MDTraj - medaka - medImgProc - MedPy - Meep - MEGA - MEGACC - MEGAHIT - Meld - MEME - memkind - memory-profiler - meRanTK - MERCKX - Mercurial - Mesa - meshio - Meson - Mesquite - MetaBAT - MetaboAnalystR - MetaGeneAnnotator - Metal - MetaPhlAn2 - metaWRAP - Metaxa2 - MethylDackel - methylpy - METIS - mhcflurry - MiGEC - MIGRATE-N - MINC - Mini-XML - Miniconda2 - Miniconda3 - minieigen - Minimac4 - minimap2 - MinPath - MIRA - miRDeep2 - MiXCR - mkl-dnn - mkl-service - mkl_fft - MLC - Mmg - MMSEQ - MMseqs2 - modred - Molcas - Molden - Molekel - molmod - Molpro - Mono - Monocle3 - mordecai - MoreRONN - mosdepth - Mothur - motif - MotionCor2 - motionSegmentation - MoviePy - MPC - MPFR - mpi4py - MPICH - MPICH2 - mpifileutils - mpiP - MPJ-Express - mpmath - MrBayes - MRIcron - MRtrix - MSM - MSPC - msprime - MTL4 - MultiNest - MultiQC - Multiwfn - MUMmer - MUMPS - muParser - MuPeXI - MUSCLE - MuSiC - MuTect - mutil - MVAPICH2 - MXNet - mygene - MyMediaLite - mympingpong - mypy - MySQL - MySQL-python - mysqlclient

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/9.3.0, GCCcore/system, system

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

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

maeparser

maeparser is a parser for Schrodinger Maestro files.

homepage: https://github.com/schrodinger/maeparser

version	toolchain
1.2.2	gompi/2019a, iimpi/2019a

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
7.453	-with-extensions	GCC/8.3.0, iccifort/2019.5.281

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

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

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

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

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

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

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

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

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

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

manta

Manta calls structural variants (SVs) and indels from mapped paired-end sequencing reads. It is optimized for analysis of germline variation in small sets of individuals and somatic variation in tumor/normal sample pairs. Manta discovers, assembles and scores large-scale SVs, medium-sized indels and large insertions within a single efficient workflow.

homepage: https://github.com/Illumina/manta

version	toolchain
1.1.1	system
1.6.0	system

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

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

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

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

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, GCCcore/8.3.0, foss/2018b

Mash

Fast genome and metagenome distance estimation using MinHash

homepage: http://mash.readthedocs.org

version	toolchain
2.0	foss/2018a
2.1	foss/2018b

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

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

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

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

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: https://www.mathworks.com/products/matlab.html

version	toolchain
2012b	system
2013b	system
2015a	system
2016a	system
2017a	system
2018b	system
2019b	system

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

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
2.2.4	-Python-2.7.16	foss/2019b, intel/2019b
2.2.5	-Python-2.7.16	foss/2019b
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, fosscuda/2019b, intel/2019b

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

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
3.6.3	system

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

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

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

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-2.7.15	foss/2019a
4.7.1	-Python-3.7.2	foss/2019a

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

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		GCCcore/8.3.0, foss/2016a, intel/2016b
14.137	-Perl-5.26.1	GCCcore/6.4.0
14.137	-Perl-5.28.0	GCCcore/7.3.0

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

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

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

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

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

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
0.11.4	-Python-3.6.6	foss/2018b
0.12.0	-Python-3.6.6	foss/2018b

medImgProc

Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation.

homepage: https://github.com/WeiXuanChan/motionSegmentation

version	versionsuffix	toolchain
2.5.7	-Python-3.7.4	foss/2019b

MedPy

MedPy is a library and script collection for medical image processing in Python, providing basic functionalities for reading, writing and manipulating large images of arbitrary dimensionality. Its main contributions are n-dimensional versions of popular image filters, a collection of image feature extractors, ready to be used with scikit-learn, and an exhaustive n-dimensional graph-cut package.

homepage: https://pypi.org/project/MedPy/

version	versionsuffix	toolchain
0.4.0	-Python-3.7.4	foss/2019b

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

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

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

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

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

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

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

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

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

MERCKX

Multilingual Entity/Resource Combiner & Knowledge eXtractor

homepage: https://github.com/madewild/MERCKX

version	versionsuffix	toolchain
20170330	-Python-2.7.13	intel/2017a

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

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

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

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
0.53.1	-Python-3.6.3	intel/2017b

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

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

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

MetaGeneAnnotator

MetaGeneAnnotator is a gene-finding program for prokaryote and phage.

homepage: http://metagene.nig.ac.jp/

version	versionsuffix	toolchain
20080819	-x86-64	system

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

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

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

Metaxa2

Metaxa2 – Identifies Small Subunit (SSU) rRNAs and classifies them taxonomically

homepage: https://microbiology.se/software/metaxa2/

version	toolchain
2.2	gompi/2019a

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
0.5.0	iccifort/2019.5.281

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

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

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

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

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

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

Mini-XML

Mini-XML is a tiny XML library that you can use to read and write XML and XML-like data files in your application without requiring large non-standard libraries.

homepage: https://www.msweet.org/mxml/

version	toolchain
2.9	GCCcore/8.2.0

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

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

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

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

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

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

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

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

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

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

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

mkl_fft

NumPy-based Python interface to Intel(R) MKL FFT functionality

homepage: https://github.com/IntelPython/mkl_fft

version	versionsuffix	toolchain
1.0.14	-Python-3.6.6	intel/2018b

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

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

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

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
10-6d92c	gompi/2019b, iimpi/2019b

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

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

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

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

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	foss/2019b, intel/2019b

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

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
6.8.0.105	GCCcore/8.3.0

Monocle3

An analysis toolkit for single-cell RNA-seq.

homepage: https://cole-trapnell-lab.github.io/monocle3/

version	versionsuffix	toolchain
0.2.0	-Python-3.7.2-R-3.6.0	foss/2019a

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

MoreRONN

MoreRONN is the spiritual successor of RONN and is useful for surveying disorder in proteins as well as designing expressible constructs for X-ray crystallography.

homepage: https://github.com/varun-ramraj/MoreRONN

version	toolchain
4.9	GCC/8.3.0

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

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

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: https://motif.ics.com/

version	toolchain
2.3.5	foss/2016a, intel/2016a
2.3.7	intel/2017a
2.3.8	GCCcore/8.3.0, foss/2017b, foss/2018a, foss/2018b, foss/2019a, intel/2017b, intel/2018a, intel/2019a

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

motionSegmentation

Motion correction, explicit spatio-temporal regularization of motion tracking, random speckles enhancement, and segmentation.

homepage: https://github.com/WeiXuanChan/motionSegmentation

version	versionsuffix	toolchain
2.7.9	-Python-3.7.4	foss/2019b

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

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

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

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

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

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

mpifileutils

MPI-Based File Utilities For Distributed Systems

homepage: https://hpc.github.io/mpifileutils/

version	toolchain
0.9.1	gompi/2019a, iimpi/2019a

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

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

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

MrBayes

MrBayes is a program for the Bayesian estimation of phylogeny.

homepage: http://mrbayes.csit.fsu.edu

version	toolchain
3.2.6	foss/2016a

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

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

MSM

Multimodal Surface Matching with Higher order Clique Reduction

homepage: https://github.com/ecr05/MSM_HOCR

version	toolchain
1.0	foss/2017b, intel/2017b

MSPC

Using combined evidence from replicates to evaluate ChIP-seq peaks

homepage: https://genometric.github.io/MSPC/

version	toolchain
3.3.1	system

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

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

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

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

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

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

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/2018b, foss/2019a, foss/2019b, intel/2019a, intel/2019b
5.2.1	-metis-seq	foss/2019a, intel/2019a

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

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

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, GCC/8.3.0

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

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

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

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

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

mygene

Python Client for MyGene.Info services.

homepage: https://github.com/biothings/mygene.py

version	toolchain
3.1.0	intel/2019a

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

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

mypy

Optional static typing for Python

homepage: http://www.mypy-lang.org/

version	toolchain
0.4.5	intel/2016b

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

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

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

N

NAG - NAGfor - NAMD - NanoComp - nanofilt - NanoFilt - nanoget - nanomath - nanonet - NanoPlot - nanopolish - NASM - NBO - NCBI-Toolkit - ncbi-vdb - NCCL - ncdf4 - ncdu - NCIPLOT - NCL - ncl - NCO - ncompress - ncurses - ncview - nd2reader - ne - NEdit - Net-core - netCDF - netCDF-C++ - netCDF-C++4 - netCDF-Fortran - netcdf4-python - netloc - NetLogo - netMHC - netMHCIIpan - netMHCpan - NetPIPE - nettle - networkx - NeuroKit - NEURON - Nextflow - NextGenMap - NFFT - nglview - NGS - NGS-Python - NGSadmix - ngspice - NiBabel - NIfTI - Nilearn - Nim - NIMBLE - Ninja - Nipype - NLopt - NLTK - Node-RED - nodejs - Normaliz - nose-parameterized - novoalign - NOVOPlasty - npstat - NRGLjubljana - NSPR - NSS - ntEdit - ntHits - numactl - numba - numexpr - numpy - nvtop - NWChem - NxTrim

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

NAGfor

The checking compiler for improved code portability and detailed error reporting.

homepage: http://www.nag.co.uk

version	toolchain
6.2.14	system

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

NanoComp

Comparing runs of Oxford Nanopore sequencing data and alignments

homepage: https://github.com/wdecoster/NanoComp

version	versionsuffix	toolchain
1.10.1	-Python-3.7.4	intel/2019b

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

NanoFilt

Filtering and trimming of Oxford Nanopore Sequencing data

homepage: https://github.com/wdecoster/nanofilt

version	versionsuffix	toolchain
2.6.0	-Python-3.7.4	intel/2019b

nanoget

Functions to extract information from Oxford Nanopore sequencing data and alignments

homepage: https://github.com/wdecoster/nanoget

version	versionsuffix	toolchain
1.12.1	-Python-3.7.4	intel/2019b

nanomath

A few simple math function for other Oxford Nanopore processing scripts

homepage: https://github.com/wdecoster/nanomath

version	versionsuffix	toolchain
0.23.1	-Python-3.7.4	intel/2019b

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

NanoPlot

Plotting suite for long read sequencing data and alignments

homepage: https://github.com/wdecoster/NanoPlot

version	versionsuffix	toolchain
1.28.4	-Python-3.7.4	intel/2019b

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

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

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

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

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

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

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
1.17		foss/2019b

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

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

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

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

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

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

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: https://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

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

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

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

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

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

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

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

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

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		gompi/2019b, iimpi/2019b

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
1.5.3	-Python-3.7.4	intel/2019b

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

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

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

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

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

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

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

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	foss/2018b, foss/2019a, 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, intel/2019b

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

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

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
19.12.0	system
20.01.0	system

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

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

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

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

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

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

ngspice

Ngspice is a mixed-level/mixed-signal circuit simulator. Its code is based on three open source software packages: Spice3f5, Cider1b1 and Xspice.

homepage: https://ngspice.sourceforge.net

version	toolchain
31	foss/2019b

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

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

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

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

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

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

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

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

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

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

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
12.16.1	GCCcore/8.3.0

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

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

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

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

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

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

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

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

ntEdit

ntEdit is a fast and scalable genomics application for polishing genome assembly drafts.

homepage: https://github.com/bcgsc/ntEdit

version	toolchain
1.3.1	iccifort/2018.3.222-GCC-7.3.0-2.30

ntHits

ntHits is a method for identifying repeats in high-throughput DNA sequencing data.

homepage: https://github.com/bcgsc/ntHits

version	toolchain
0.0.1	iccifort/2018.3.222-GCC-7.3.0-2.30

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

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
0.47.0	-Python-3.7.4	foss/2019b, fosscuda/2019b

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/en/latest/

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
2.7.1	-Python-2.7.16	intel/2019b
2.7.1	-Python-3.7.4	foss/2019b

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

nvtop

htop-like GPU usage monitor

homepage: https://github.com/Syllo/nvtop

version	toolchain
1.0.0	fosscuda/2018b

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

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

O

Oases - OBITools - OCaml - occt - OCNet - Octave - OMA - OOMPA - OPARI2 - OpenAI-Gym - OpenBabel - OpenBLAS - OpenCoarrays - OpenColorIO - OpenCV - opencv_contrib - OpenEXR - OpenFOAM - OpenFOAM-Extend - OpenImageIO - OpenJPEG - OpenKIM-API - openkim-models - OpenMM - OpenMolcas - OpenMPI - OpenNLP - OpenPGM - OpenPIV - openpyxl - OpenPyXL - OpenRefine - OpenSlide - openslide-python - OpenSSL - OPERA - OptiType - OptiX - OR-Tools - orca - ORCA - OrfM - OrthoFinder - OrthoMCL - Osi - OSU-Micro-Benchmarks - OTF2 - ownCloud - oxford_asl

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

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

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

occt

Open CASCADE Technology (OCCT) is an object-oriented C++ class library designed for rapid production of sophisticated domain-specific CAD/CAM/CAE applications.

homepage: https://www.opencascade.com/

version	toolchain
7.3.0p4	foss/2019b

OCNet

Generate and analyze Optimal Channel Networks (OCNs): oriented spanning trees reproducing all scaling features characteristic of real, natural river networks. As such, they can be used in a variety of numerical experiments in the fields of hydrology, ecology and epidemiology.

homepage: https://cran.r-project.org/web/packages/OCNet

version	versionsuffix	toolchain
0.2.0	-R-3.6.0	foss/2019a

Octave

GNU Octave is a high-level interpreted language, primarily intended for numerical computations.

homepage: https://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
5.1.0		foss/2019a, foss/2019b

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

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

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

OpenAI-Gym

A toolkit for developing and comparing reinforcement learning algorithms.

homepage: https://gym.openai.com

version	versionsuffix	toolchain
0.17.1	-Python-3.7.4	foss/2019b

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: https://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
2.4.1	-Python-3.7.2	intel/2019a
3.0.0	-Python-3.7.4	gompi/2019b

OpenBLAS

OpenBLAS is an optimized BLAS library based on GotoBLAS2 1.13 BSD version.

homepage: https://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
0.3.8		GCC/9.2.0

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

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

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: https://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
4.2.0	-Python-3.7.4	foss/2019b, fosscuda/2019b

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: https://opencv.org/

version	versionsuffix	toolchain
3.4.1	-Python-3.6.4	foss/2018a

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

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, intel/2019b
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, intel/2019b

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
4.1-20191120	-Python-2.7.16	intel/2019b

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

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

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

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, foss/2019b, intel/2019a, intel/2019b

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

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

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

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

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

OpenPIV

OpenPIV is an open source Particle Image Velocimetry analysis software

homepage: http://www.openpiv.net

version	versionsuffix	toolchain
0.21.8	-Python-3.7.4	intel/2019b

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

OpenPyXL

A Python library to read/write Excel 2010 xlsx/xlsm files

homepage: https://openpyxl.readthedocs.io

version	toolchain
2.6.4	GCCcore/8.3.0

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

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

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

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

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

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

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

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

orca

Orca is an Electron app that generates images and reports of Plotly things like plotly.js graphs, dash apps, dashboards from the command line.

homepage: https://github.com/plotly/orca

version	toolchain
1.3.0	GCCcore/8.3.0

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

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

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
2.3.8	-Python-2.7.16	foss/2019b
2.3.11	-Python-3.7.4	intel/2019b

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

Osi

Osi (Open Solver Interface) provides an abstract base class to a generic linear programming (LP) solver, along with derived classes for specific solvers. Many applications may be able to use the Osi to insulate themselves from a specific LP solver. That is, programs written to the OSI standard may be linked to any solver with an OSI interface and should produce correct results. The OSI has been significantly extended compared to its first incarnation. Currently, the OSI supports linear programming solvers and has rudimentary support for integer programming.

homepage: https://github.com/coin-or/Osi

version	toolchain
0.108.5	GCCcore/7.3.0

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

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

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

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

P

p11-kit - p4est - p4vasp - p7zip - packmol - PAML - pandas - pandas-datareader - PANDAseq - Pandoc - Pango - PAPI - parallel - parallel-fastq-dump - ParallelIO - parasail - Paraver - ParaView - PARI-GP - ParmEd - ParMETIS - ParMGridGen - PartitionFinder - pasta - PaStiX - patchelf - path.py - pauvre - pbbam - pbcopper - pbdagcon - pbmm2 - pbs_python - PBSuite - PCAngsd - PCC - PCL - PCMSolver - PCRaster - PCRE - PCRE2 - PDT - PEAR - Perl - perl-app-cpanminus - Perl4-CoreLibs - PETSc - petsc4py - pftoolsV3 - pFUnit - PGDSpider - PGI - PHASE - PHAST - PheWAS - PhiPack - PHLAT - phono3py - phonopy - PHYLIP - PhyloBayes-MPI - phylokit - phylonaut - PhyML - phyx - picard - pigz - PIL - PileOMeth - Pillow - Pillow-SIMD - Pilon - PIMS - Pindel - pip - Pisces - piSvM - piSvM-JSC - pixman - pizzly - pkg-config - pkgconfig - PlaScope - PLAST - Platanus - Platypus - plc - PLINK - PLINKSEQ - Ploticus - plotly - plotly.py - PLplot - PLUMED - PLY - PMIx - PnetCDF - pocl - polymake - pomkl - pompi - poppler - popt - Porechop - poretools - Postgres-XL - PostgreSQL - POT - POV-Ray - PPfold - ppl - pplacer - pplpy - PRANK - PRC - preseq - pretty-yaml - Primer3 - PRINSEQ - printproto - PRISMS-PF - ProbABEL - prodigal - PROJ - ProjectQ - prokka - prompt-toolkit - proovread - propy - Proteinortho - protobuf - protobuf-python - PRSice - pscom - PSI - PSI4 - psmc - psmpi - psmpi2 - PSolver - PSORTb - psrecord - pstoedit - psutil - psycopg2 - ptemcee - PTESFinder - pubtcrs - pullseq - py - py-cpuinfo - PyAMG - PyAPS3 - pybedtools - pyBigWig - pybind11 - PyCairo - PyCharm - pycma - pycodestyle - PyCogent - PyCUDA - PyDatastream - pydicom - pydlpoly - pydot - pyEGA3 - pyenchant - PyFFmpeg - pyFFTW - pyfits - PyFMI - PyFR - pygccxml - pyGIMLi - Pygments - PyGObject - pygraphviz - pygrib - PyGTK - PyGTS - PyGWAS - pyhdf - pyiron - Pyke3 - pylift - Pylint - pymatgen - pymatgen-db - pymbar - PyMC3 - pymemcache - PyNAST - Pyomo - PyOpenGL - pyparsing - pyplusplus - pyproj - pyqstem - PyQt - PyQt5 - PyQtGraph - PyRe - PyRETIS - pyringe - Pyro4 - Pysam - pyScaf - PySCF - pyshp - Pysolar - pysqlite - PyStan - pystran - PyTables - pytest - PYTHIA - Python - python-igraph - python-Levenshtein - python-parasail - python-weka-wrapper3 - pythran - PyTorch - PyTorch-Geometric - PyYAML - PyZMQ

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

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

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

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

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

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

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

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

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

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

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
1.44.7	GCCcore/8.3.0

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

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

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

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

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
2.4.1	intel/2019b

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

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, intel/2019b

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

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

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, gompi/2019b, iimpi/2019a, iimpi/2019b, intel/2016a, intel/2016b, intel/2017a, intel/2017b, intel/2018a, intel/2018b

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

PartitionFinder

PartitionFinder 2 is a Python program for simultaneously choosing partitioning schemes and models of molecular evolution for phylogenetic analyses of DNA, protein, and morphological data. You can PartitionFinder 2 before running a phylogenetic analysis, in order to decide how to divide up your sequence data into separate blocks before analysis, and to simultaneously perform model selection on each of those blocks.

homepage: https://www.robertlanfear.com/partitionfinder

version	versionsuffix	toolchain
2.1.1	-Python-2.7.16	intel/2019b

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

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

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

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

pauvre

Tools for plotting Oxford Nanopore and other long-read data

homepage: https://github.com/conchoecia/pauvre

version	versionsuffix	toolchain
0.1923	-Python-3.7.4	intel/2019b

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

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

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

pbmm2

A minimap2 frontend for PacBio native data formats

homepage: https://github.com/PacificBiosciences/pbmm2

version	toolchain
1.1.0	gompi/2019a

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

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

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

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

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

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

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

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

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

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

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

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

perl-app-cpanminus

cpanm - get, unpack build and install modules from CPAN

homepage: https://github.com/miyagawa/cpanminus

version	toolchain
1.7039	system

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

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
3.12.3		foss/2019b
3.12.4		foss/2019b, intel/2019b

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

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

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

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

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
19.10	-GCC-8.3.0-2.32	system

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

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

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

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

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

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

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

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

PhyloBayes-MPI

A Bayesian software for phylogenetic reconstruction using mixture models

homepage: https://github.com/bayesiancook/pbmpi

version	toolchain
20161021	intel/2016b

phylokit

C++ library for high performance phylogenetics

homepage: https://github.com/pranjalv123/phylokit

version	toolchain
1.0	GCC/8.2.0-2.31.1

phylonaut

Dynamic programming for phylogenetics applications

homepage: https://github.com/pranjalv123/phylonaut

version	toolchain
20190626	gompi/2019a

PhyML

Phylogenetic estimation using (Maximum) Likelihood

homepage: https://github.com/stephaneguindon/phyml

version	toolchain
3.3.20190321	foss/2018b

phyx

phyx performs phylogenetics analyses on trees and sequences.

homepage: https://github.com/FePhyFoFum/phyx

version	toolchain
1.01	foss/2019a

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM format.

homepage: https://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
2.21.6	-Java-11	system

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, GCCcore/8.3.0, foss/2018a

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

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

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

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

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

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

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

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

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

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

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

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

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

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/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0, GCCcore/8.3.0, intel/2017a, system

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

PlaScope

Plasmid exploration of bacterial genomes

homepage: https://github.com/GuilhemRoyer/PlaScope

version	toolchain
1.3.1	foss/2018b

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

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

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

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

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

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

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

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

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

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

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	foss/2019b, intel/2019b
2.5b	-Python-2.7.14	intel/2018a

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

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/7.2.0, GCCcore/7.3.0
2.2.1	GCCcore/7.2.0, GCCcore/7.3.0, GCCcore/8.2.0
2.2.3	GCCcore/7.2.0, 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

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

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

polymake

polymake is open source software for research in polyhedral geometry. It deals with polytopes, polyhedra and fans as well as simplicial complexes, matroids, graphs, tropical hypersurfaces, and other objects.

homepage: https://polymake.org

version	toolchain
4.0r1	foss/2019b

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

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

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

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

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
0.2.4	-Python-3.7.4	intel/2019b

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

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

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

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

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

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

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

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

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

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

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

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

pretty-yaml

PyYAML-based python module to produce pretty and readable YAML-serialized data. This module is for serialization only, see ruamel.yaml module for literate YAML parsing (keeping track of comments, spacing, line/column numbers of values, etc).

homepage: https://github.com/mk-fg/pretty-yaml

version	toolchain
19.12.0	GCCcore/8.3.0

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

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

printproto

X.org PrintProto protocol headers.

homepage: http://xorg.freedesktop.org/

version	toolchain
1.0.5	intel/2016a

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

ProbABEL

Tool for genome-wide association analysis of imputed genetic data.

homepage: http://www.genabel.org/packages/ProbABEL

version	toolchain
0.5.0	system

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

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

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

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

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

proovread

PacBio hybrid error correction through iterative short read consensus

homepage: https://github.com/BioInf-Wuerzburg/proovread

version	toolchain
2.14.1	intel/2017b

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

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

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

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

PRSice

PRSice (pronounced ‘precise’) is a Polygenic Risk Score software for calculating, applying, evaluating and plotting the results of polygenic risk scores (PRS) analyses.

homepage: https://www.prsice.info/

version	toolchain
2.2.12	GCCcore/8.3.0

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

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

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

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

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

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

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

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

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

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

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

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

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

PTESFinder

Post-Transcriptional Exon Shuffling (PTES) Identification Pipeline

homepage: https://sourceforge.net/projects/ptesfinder-v1/

version	toolchain
1	intel/2017b

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

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

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

py-cpuinfo

py-cpuinfo gets CPU info with pure Python.

homepage: https://github.com/workhorsy/py-cpuinfo

version	toolchain
5.0.0	system

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

PyAPS3

Python 3 Atmospheric Phase Screen

homepage: https://github.com/AngeliqueBenoit/pyaps3

version	versionsuffix	toolchain
20190407	-Python-3.7.2	foss/2019a

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

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

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

PyCairo

Python bindings for the cairo library

homepage: https://pycairo.readthedocs.io/

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
1.18.2		GCCcore/8.3.0

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

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

pycodestyle

pycodestyle is a tool to check your Python code against some of the style conventions in PEP 8.

homepage: https://pycodestyle.readthedocs.io

version	versionsuffix	toolchain
2.5.0	-Python-3.6.4	intel/2018a

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

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

PyDatastream

Lightweight SOAP client

homepage: https://pypi.python.org/pypi/suds-py3

version	versionsuffix	toolchain
0.5.1	-Python-3.6.4	intel/2018a

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
1.4.2		GCCcore/8.3.0

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

pydot

Python interface to Graphviz’s Dot language.

homepage: https://github.com/pydot/pydot

version	toolchain
1.4.1	foss/2019b

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

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

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

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	versionsuffix	toolchain
0.11.1		intel/2019a
0.11.1	-Python-3.6.6	foss/2018b

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

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

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

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

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

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

PyGObject

PyGObject is a Python package which provides bindings for GObject based libraries such as GTK, GStreamer, WebKitGTK, GLib, GIO and many more.

homepage: https://pygobject.readthedocs.io/

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-2.7.16	GCCcore/8.3.0
3.34.0	-Python-3.7.2	GCCcore/8.2.0
3.34.0	-Python-3.7.4	GCCcore/8.3.0

pygraphviz

PyGraphviz is a Python interface to the Graphviz graph layout and visualization package. With PyGraphviz you can create, edit, read, write, and draw graphs using Python to access the Graphviz graph data structure and layout algorithms.

homepage: https://pygraphviz.github.io/

version	toolchain
1.5	foss/2019b

pygrib

Python interface for reading and writing GRIB data

homepage: https://jswhit.github.io/pygrib

version	toolchain
2.0.4	foss/2019a

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

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

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

pyhdf

Python wrapper around the NCSA HDF version 4 library

homepage: https://github.com/fhs/pyhdf

version	toolchain
0.10.1	foss/2019a

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

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

pylift

pylift is an uplift library that provides, primarily: (1) Fast uplift modeling implementations and (2) Evaluation tools (UpliftEval class).

homepage: https://github.com/df-foundation/pylift

version	versionsuffix	toolchain
0.1.5	-Python-3.7.4	foss/2019b

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

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

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

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

PyMC3

Probabilistic Programming in Python: Bayesian Modeling and Probabilistic Machine Learning with Theano

homepage: https://docs.pymc.io/

version	versionsuffix	toolchain
3.8	-Python-3.7.4	intel/2019b

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

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

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

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

pyparsing

The pyparsing module is an alternative approach to creating and executing simple grammars, vs. the traditional lex/yacc approach, or the use of regular expressions. The pyparsing module provides a library of classes that client code uses to construct the grammar directly in Python code.

homepage: https://github.com/pyparsing/pyparsing

version	versionsuffix	toolchain
2.4.6	-Python-2.7.16	GCCcore/8.3.0

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

pyproj

Python interface to PROJ4 library for cartographic transformations

homepage: https://pyproj4.github.io/pyproj

version	versionsuffix	toolchain
2.1.3		GCCcore/8.2.0
2.4.2	-Python-3.7.4	GCCcore/8.3.0

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

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

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, intel/2018b
5.12.1	-Python-2.7.15	GCCcore/8.2.0
5.12.1	-Python-3.7.2	GCCcore/8.2.0

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-3.6.6	foss/2018b, intel/2018b
0.10.0	-Python-3.7.2	intel/2019a

PyRe

PyRe (Python Reliability) is a Python module for structural reliability analysis.

homepage: https://hackl.science/pyre

version	versionsuffix	toolchain
5.0.3-20190221	-Python-3.7.4	foss/2019b, intel/2019b

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

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

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

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

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

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

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

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

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

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

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

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: https://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
3.5.2	-Python-2.7.16	intel/2019b
3.6.1	-Python-3.7.4	foss/2019b

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

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

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

python-igraph

Python interface to the igraph high performance graph library, primarily aimed at complex network research and analysis.

homepage: https://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
0.8.0		foss/2019b

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

python-parasail

Python Bindings for the Parasail C Library

homepage: https://github.com/jeffdaily/parasail-python

version	versionsuffix	toolchain
1.1.12	-Python-2.7.14	intel/2018a
1.1.16	-Python-3.6.6	foss/2018b
1.2	-Python-3.7.4	intel/2019b

python-weka-wrapper3

Python3 wrapper for the Weka Machine Learning Workbench

homepage: https://github.com/fracpete/python-weka-wrapper3

version	versionsuffix	toolchain
0.1.11	-Python-3.7.4	foss/2019b

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

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
1.4.0	-Python-3.7.4	foss/2019b, fosscuda/2019b

PyTorch-Geometric

PyTorch Geometric (PyG) is a geometric deep learning extension library for PyTorch.

homepage: https://github.com/rusty1s/pytorch_geometric

version	versionsuffix	toolchain
1.3.2	-Python-3.7.4	foss/2019b
1.4.2	-Python-3.7.4-PyTorch-1.4.0	foss/2019b

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

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

Q

Q6 - QCA - qcat - qcint - QDD - QEMU - QGIS - Qhull - QIIME - QIIME2 - Qiskit - QJson - QML - qpth - qrupdate - QScintilla - Qt - Qt5 - Qt5Webkit - QtKeychain - QTLtools - qtop - Qualimap - Quandl - QuantumESPRESSO - QUAST - QuaZIP - QuickFF - Quip - Quorum - QuTiP - Qwt - QwtPolar

Q6

EVB, FEP and LIE simulator.

homepage: https://github.com/qusers/Q6

version	toolchain
20180205	gompi/2019a

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

qcat

qcat is a Python command-line tool for demultiplexing Oxford Nanopore reads from FASTQ files

homepage: https://github.com/nanoporetech/qcat/releases

version	versionsuffix	toolchain
1.1.0	-Python-3.7.4	intel/2019b

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

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

QEMU

QEMU is a generic and open source machine emulator and virtualizer.

homepage: https://www.qemu.org/

version	toolchain
2.10.1	intel/2017b

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

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
2019.1	GCCcore/8.2.0, GCCcore/8.3.0

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

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

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

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

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

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

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, GCC/8.2.0-2.31.1, GCCcore/6.4.0, GCCcore/8.3.0, foss/2016a, foss/2018a, foss/2018b, intel/2016a, intel/2016b, intel/2017a

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

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

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, intel/2018b
5.11.2	foss/2018b
5.12.3	GCCcore/8.2.0
5.13.1	GCCcore/8.3.0

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

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

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

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

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

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

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
6.5		intel/2019a

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

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

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

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

Quorum

QuorUM is an error corrector for Illumina reads

homepage: http://www.genome.umd.edu/quorum.html

version	toolchain
1.1.1	intel/2017a

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

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

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

R

R - R-bundle-Bioconductor - R-keras - R-tesseract - Racon - Ragout - randfold - randrproto - RapidJSON - rapidtide - Rascaf - RASPA2 - RAxML - RAxML-NG - Ray - RBFOpt - rclone - Rcorrector - rCUDA - RDFlib - RDKit - RDP-Classifier - re2c - Reads2snp - Red - Redundans - ReFrame - RELION - REMORA - renderproto - RepastHPC - RepeatMasker - requests - RERconverge - rgdal - rgeos - rhdf5 - rioxarray - rjags - Rmath - RMBlast - RNA-SeQC - RNAclust - RNAcode - RNAIndel - rnaQUAST - RNAz - Roary - ROI_PAC - ROME - ROOT - rootpy - Rosetta - rpmrebuild - rpy2 - RQGIS3 - RSEM - RSeQC - RStan - rstanarm - RTG-Tools - Rtree - Ruby - Rust

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

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
3.10		foss/2019b

R-keras

Interface to ‘Keras’ <https://keras.io>, 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
2.2.5.0	-Python-3.7.4-R-3.6.2	foss/2019b, fosscuda/2019b

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

Racon

Ultrafast consensus module for raw de novo genome assembly of long uncorrected reads

homepage: https://github.com/clara-genomics/racon-gpu

version	toolchain
1.3.2	GCCcore/8.2.0
1.4.7	GCCcore/8.2.0, gcccuda/2019b
1.4.10	GCC/7.3.0-2.30

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

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

randrproto

Xrandr protocol and ancillary headers

homepage: http://www.freedesktop.org/wiki/Software/xlibs

version	toolchain
1.5.0	foss/2016a, intel/2016a

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, GCCcore/8.3.0

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

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

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

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	iimpi/2019b, intel/2019a

RAxML-NG

RAxML-NG is a phylogenetic tree inference tool which uses maximum-likelihood (ML) optimality criterion. Its search heuristic is based on iteratively performing a series of Subtree Pruning and Regrafting (SPR) moves, which allows to quickly navigate to the best-known ML tree.

homepage: https://github.com/amkozlov/raxml-ng

version	toolchain
0.9.0	gompi/2019b

Ray

Parallel genome assemblies for parallel DNA sequencing

homepage: http://denovoassembler.sourceforge.net/

version	toolchain
2.3.1	iimpi/2019a

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

rclone

Rclone is a command line program to sync files and directories to and from a variety of online storage services

homepage: https://rclone.org/

version	versionsuffix	toolchain
1.42	-amd64	system

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

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

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	GCCcore/8.3.0, foss/2019a

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
2019.09.3	-Python-3.7.4	foss/2019b

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

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

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

Red

Red (REpeat Detector)

homepage: http://toolsmith.ens.utulsa.edu/

version	toolchain
2015-05-22	iccifort/2019.1.144-GCC-8.2.0-2.31.1

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

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
2.21	system

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

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

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

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

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

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

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

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
1.4-8	-R-3.6.2	foss/2019b

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
0.5-2	-R-3.6.2	foss/2019b

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

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

rjags

The rjags package is an interface to the JAGS library.

homepage: https://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
4-9	-R-3.6.0	foss/2019a

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

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

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

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

RNAcode

RNAcode - Analyze the protein coding potential in multiple sequence alignments

homepage: https://wash.github.io/rnacode/

version	toolchain
0.3	foss/2017a

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

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

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

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

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

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

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
6.14.06	-Python-3.6.6	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

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

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

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

rpy2

rpy2 is an interface to R running embedded in a Python process.

homepage: https://rpy2.bitbucket.io/

version	versionsuffix	toolchain
2.7.9	-Python-2.7.12	foss/2016b
2.8.2	-Python-2.7.13	intel/2017a
3.2.6	-Python-3.7.4	foss/2019b

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

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

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

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

rstanarm

Estimates previously compiled regression models using the ‘rstan’ package, which provides the R interface to the Stan C++ library for Bayesian estimation.

homepage: https://r-forge.r-project.org/projects/rstanarm

version	versionsuffix	toolchain
2.19.3	-R-3.6.2	foss/2019b

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

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

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
2.7.1	GCCcore/8.3.0

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

S

S-Lang - S4 - SAGE - Sailfish - SALib - Salmon - SALMON-TDDFT - Sambamba - Samcef - samclip - SAMtools - SAS - savvy - Saxon-HE - sbt - ScaLAPACK - Scalasca - SCALCE - sciClone - ScientificPython - scikit-allel - scikit-build - scikit-image - scikit-learn - scikit-multilearn - scikit-optimize - SCIPhI - scipy - SciPy-bundle - SCnorm - Scoary - SCons - SCOOP - Score-P - SCOTCH - scp - Scrappie - scVelo - SDCC - SDL2 - Seaborn - SearchGUI - SECAPR - segemehl - segmentation-models - SelEstim - SentencePiece - sep - SEPP - Seq-Gen - seq2HLA - SeqAn - SeqAn3 - Seqmagick - SeqPrep - seqtk - Serf - setuptools - Seurat - Shannon - shapAAR - SHAPEIT - Shapely - sharutils - shift - SHORE - Short-Pair - shovill - shrinkwrap - Sibelia - sickle - Siesta - SimPEG - SIMPLE - SimpleElastix - SimpleITK - simpy - SimVascular - SingleM - Singular - Singularity - SIONlib - SIP - SKESA - sketchmap - skewer - SLATEC - SLEPc - slepc4py - sleuth - slidingwindow - smafa - smallgenomeutilities - SMARTdenovo - Smoldyn - SMRT-Link - snakemake - SNAP - SNAPE-pooled - snaphu - snappy - snippy - snpEff - SNPhylo - SOAPaligner - SOAPdenovo-Trans - SOAPdenovo2 - SOAPfuse - socat - SolexaQA++ - SortMeRNA - Spack - SPAdes - spaln - Spark - sparsehash - spatialreg - spectral.methods - spglib - spglib-python - Sphinx - SpiceyPy - SpiecEasi - SPLASH - SpliceMap - split-seq - splitRef - spoa - SPRNG - Spyder - SQLite - SqueezeMeta - SRA-Toolkit - SRPRISM - SSAHA2 - SSN - SSPACE_Basic - Stacks - STAMP - StaMPS - Stampy - STAR - STAR-Fusion - Stata - statsmodels - STEAK - STIR - stpipeline - STREAM - strelka - StringTie - Structure - Subread - Subversion - suds - SuiteSparse - SUMACLUST - SUMATRA - SUNDIALS - SuperLU - supermagic - supernova - SVDetect - SVDquest - SVG - swarm - SWASH - SWIG - SymEngine - sympy - Szip

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

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

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

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		gompi/2019b
0.10.1	-Python-2.7.12	foss/2016b

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

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, gompi/2019b
1.1.0		gompi/2019b

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

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

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

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

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		GCC/8.3.0, foss/2018b, intel/2017a, intel/2017b, intel/2018a, intel/2018b, intel/2019b
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, GCC/8.3.0, iccifort/2019.5.281

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

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

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

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

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

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

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

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

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

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

scikit-build

Scikit-Build, or skbuild, is an improved build system generator for CPython C/C++/Fortran/Cython extensions.

homepage: https://scikit-build.github.io

version	versionsuffix	toolchain
0.10.0	-Python-3.6.6	foss/2018b, intel/2018b

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, fosscuda/2019b

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
0.20.4	-Python-2.7.16	intel/2019b
0.21.3	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b

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

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
0.7.4	-Python-3.7.4	foss/2019b

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

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

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, intel/2019b
2019.10	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b

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

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

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

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

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

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

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

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

scVelo

scVelo is a scalable toolkit for estimating and analyzing RNA velocities in single cells using dynamical modeling.

homepage: https://scvelo.org

version	versionsuffix	toolchain
0.1.24	-Python-3.7.4	foss/2019b

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

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

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
0.10.0	-Python-3.7.4	foss/2019b, intel/2019b

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

SECAPR

SECAPR is a bioinformatics pipeline for the rapid and user-friendly processing of targeted enriched Illumina sequences, from raw reads to alignments

homepage: https://github.com/AntonelliLab/seqcap_processor

version	versionsuffix	toolchain
1.1.15	-Python-2.7.16	foss/2019b

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

segmentation-models

Python library with Neural Networks for Image Segmentation based on Keras and TensorFlow.

homepage: https://github.com/qubvel/segmentation_models

version	versionsuffix	toolchain
1.0.1	-Python-3.7.4	foss/2019b, fosscuda/2019b

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

SentencePiece

Unsupervised text tokenizer for Neural Network-based text generation.

homepage: https://github.com/google/sentencepiece

version	versionsuffix	toolchain
0.1.85	-Python-3.7.4	GCC/8.3.0

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

SEPP

SATe-enabled Phylogenetic Placement - addresses the problem of phylogenetic placement of short reads into reference alignments and trees.

homepage: https://github.com/smirarab/sepp

version	versionsuffix	toolchain
4.3.10	-Python-3.7.4	foss/2019b

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

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

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	versionsuffix	toolchain
1.4.2	-library	system
2.3.2		foss/2016b
2.4.0		GCC/8.2.0-2.31.1, foss/2018b, intel/2018b

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

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

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

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, GCC/8.3.0, foss/2018a, foss/2018b

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

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

Seurat

Seurat is an R package designed for QC, analysis, and exploration of single cell RNA-seq data.

homepage: https://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
3.1.2	-R-3.6.0	foss/2019a

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

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

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

Shapely

Shapely is a BSD-licensed Python package for manipulation and analysis of planar geometric objects. It is based on the widely deployed GEOS (the engine of PostGIS) and JTS (from which GEOS is ported) libraries.

homepage: https://github.com/Toblerity/Shapely

version	versionsuffix	toolchain
1.7.0	-Python-3.7.4	GCC/8.3.0, iccifort/2019.5.281

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

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

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

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

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

shrinkwrap

A std::streambuf wrapper for compression formats.

homepage: https://github.com/jonathonl/shrinkwrap

version	toolchain
1.0.0-beta	GCCcore/8.2.0

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

sickle

Windowed Adaptive Trimming for fastq files using quality

homepage: https://github.com/najoshi/sickle

version	toolchain
1.33	foss/2017a, intel/2018a

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	versionsuffix	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
4.1-MaX-1.0		intel/2019b
4.1-MaX-1.0	-PEXSI	intel/2019b

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

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

SimpleElastix

Multi-lingual medical image registration library.

homepage: https://simpleelastix.github.io

version	versionsuffix	toolchain
0.10.0	-Python-3.6.3	foss/2017b
0.10.0	-Python-3.6.4	foss/2018a
1.1.0	-Python-3.7.4	foss/2019b

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
1.2.4	-Python-3.7.4	foss/2019b

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

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

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

Singular

Singular is a computer algebra system for polynomial computations, with special emphasis on commutative and non-commutative algebra, algebraic geometry, and singularity theory.

homepage: https://www.singular.uni-kl.de/

version	toolchain
4.1.2	system

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

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

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

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

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

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

SLATEC

SLATEC Common Mathematical Library, a comprehensive software library containing over 1400 general purpose mathematical and statistical routines written in Fortran 77.

homepage: https://www.netlib.org/slatec/

version	toolchain
4.1	GCC/6.4.0-2.28, iccifort/2018.1.163-GCC-6.4.0-2.28

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: https://www.grycap.upv.es/slepc/

version	toolchain
3.8.3	foss/2017b
3.9.2	foss/2018a
3.11.0	foss/2018b
3.12.2	foss/2019b, intel/2019b

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

SPAdes

Genome assembler for single-cell and isolates data sets

homepage: http://bioinf.spbau.ru/en/spades

version	versionsuffix	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
3.14.0	-Python-3.7.2	GCC/8.2.0-2.31.1
3.14.0	-Python-3.7.4	GCC/8.3.0

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

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

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, GCCcore/8.3.0, foss/2016b, intel/2017a

spatialreg

A collection of all the estimation functions for spatial cross-sectional models (on lattice/areal data using spatial weights matrices) contained up to now in ‘spdep’, ‘sphet’ and ‘spse’.

homepage: https://cran.r-project.org/package=spatialreg

version	versionsuffix	toolchain
1.1-5	-R-3.6.2	foss/2019b

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

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

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

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

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

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

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

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

split-seq

Analysis tools for split-seq.

homepage: https://github.com/yjzhang/split-seq-pipeline

version	versionsuffix	toolchain
20190717	-Python-3.6.6	foss/2018b

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

spoa

Spoa (SIMD POA) is a c++ implementation of the partial order alignment (POA) algorithm which is used to generate consensus sequences

homepage: https://github.com/rvaser/spoa

version	toolchain
3.0.1	GCC/7.3.0-2.30

SPRNG

Scalable Parallel Pseudo Random Number Generators Library

homepage: http://www.sprng.org/

version	toolchain
2.0b	foss/2016a

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

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

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

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

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

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

SSN

Spatial statistical modeling and prediction for data on stream networks, including models based on in-stream distance. Models are created using moving average constructions. Spatial linear models, including explanatory variables, can be fit with (restricted) maximum likelihood. Mapping and other graphical functions are included.

homepage: https://cran.r-project.org/web/packages/SSN

version	versionsuffix	toolchain
1.1.14	-R-3.6.0	foss/2019a

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

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
2.5	iccifort/2019.5.281
2.41	GCC/8.2.0-2.31.1, foss/2018b, iccifort/2019.1.144-GCC-8.2.0-2.31.1

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

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

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

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
2.7.2b	GCC/8.3.0
2.7.3a	GCC/8.3.0

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
1.8.1	-Python-3.7.4	foss/2019b

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	versionsuffix	toolchain
15		system
16	-legacy	system

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
0.9.0	-Python-3.6.6	intel/2018b
0.10.1		foss/2019a
0.11.0	-Python-3.7.4	foss/2019b, intel/2019b

STEAK

Detects integrations of any sort in high-throughput sequencing (HTS) data. STEAK was built for validating and discovering transposable element (TE) and retroviral integrations in a variety of HTS data. The software performs on both single-end (SE) and paired-end ( PE) libraries and on a variety of HTS sequencing strategies. It can be applied to a broad range of research interests and clinical uses such as population genetic studies and detecting polymorphic integrations.

homepage: https://omictools.com/steak-tool

version	versionsuffix	toolchain
2019.09.12	-Python-2.7.16	foss/2019b

STIR

Software for Tomographic Image Reconstruction

homepage: http://stir.sourceforge.net/

version	toolchain
3.0	intel/2018a

stpipeline

The ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format to generated datasets for down-stream analysis. The ST pipeline can also be used to process single cell data as long as a file with barcodes identifying each cell is provided. The ST Pipeline can also process RNA-Seq datasets generated with or without UMIs.

homepage: https://github.com/SpatialTranscriptomicsResearch/st_pipeline

version	versionsuffix	toolchain
1.7.3	-Python-2.7.15	foss/2018b
1.7.6	-Python-3.7.2	foss/2019a

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

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

StringTie

StringTie is a fast and highly efficient assembler of RNA-Seq alignments into potential transcripts

homepage: https://ccb.jhu.edu/software/stringtie/

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
2.1.0	foss/2018b

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	GCC/8.2.0-2.31.1, iccifort/2019.3.199-GCC-8.3.0-2.32

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, GCC/8.3.0

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

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

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, intel/2019b

SUMACLUST

SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences.

homepage: http://metabarcoding.org/sumatra

version	toolchain
1.0.20	foss/2016a

SUMATRA

SUMATRA and SUMACLUST: fast and exact comparison and clustering of sequences.

homepage: http://metabarcoding.org/sumatra

version	toolchain
1.0.20	foss/2016a

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

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

supermagic

Very simple MPI sanity code. Nothing more, nothing less.

homepage: https://github.com/hpc/supermagic

version	toolchain
20170824	foss/2017a, gompi/2019b

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

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

SVDquest

SVDquartets-based species trees

homepage: https://github.com/pranjalv123/SVDquest

version	toolchain
20190627	gompi/2019a

SVG

Perl binding for SVG

homepage: https://metacpan.org/pod/SVG

version	versionsuffix	toolchain
2.84	-Perl-5.30.0	foss/2019b

swarm

A robust and fast clustering method for amplicon-based studies

homepage: https://github.com/torognes/swarm

version	toolchain
2.2.2	foss/2018b

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

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

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

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

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

T

tabix - taco - TagLib - TAMkin - taxator-tk - tbb - tbl2asn - TCC - Tcl - tcsh - tecplot360ex - TensorFlow - TensorRT - Tesla-Deployment-Kit - tesseract - testpath - TetGen - TEToolkit - texinfo - Text-CSV - Theano - THetA - thurstonianIRT - TiCCutils - Tika - TiMBL - time - TINKER - TinyDB - Tk - Tkinter - TM-align - tmux - ToFu - Togl - TopHat - torchtext - torchvision - TotalView - tqdm - Tracer - TransDecoder - Transrate - travis - TreeMix - TreeShrink - TRF - Triangle - Trilinos - Trim_Galore - trimAl - Trimmomatic - Trinity - TRIQS - TRIQS-cthyb - TRIQS-dft_tools - TRIQS-tprf - TRUST - TurboVNC - TVB - tvb-data - TVB-deps - tvb-framework - tvb-library

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

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

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

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

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

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
2020.2	GCCcore/8.3.0

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

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

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

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

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

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
1.15.2	-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
2.0.1	-Python-3.7.2	foss/2019a
2.0.1	-Python-3.7.4	fosscuda/2019b
2.1.0	-Python-3.7.4	foss/2019b, fosscuda/2019b

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

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

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

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

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

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

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

Text-CSV

Text-CSV parser

homepage: https://metacpan.org/pod/Text::CSV

version	versionsuffix	toolchain
1.33	-Perl-5.22.1	foss/2016a

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
1.0.4	-Python-3.7.4	foss/2019b, fosscuda/2019b, intel/2019b

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

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

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

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

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

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

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

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

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

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
2.7.16		GCCcore/8.3.0
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

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

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

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

Togl

A Tcl/Tk widget for OpenGL rendering.

homepage: https://sourceforge.net/projects/togl/

version	toolchain
2.0	GCCcore/8.3.0

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

torchtext

Data loaders and abstractions for text and NLP

homepage: https://github.com/pytorch/text

version	versionsuffix	toolchain
0.5.0	-PyTorch-1.4.0--Python-3.7.4	fosscuda/2019b

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

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

tqdm

Instantly make your loops show a smart progress meter.

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
4.41.1		GCCcore/8.3.0
4.41.1	-Python-3.6.6	foss/2018b, intel/2018b

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

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

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

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

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

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

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

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

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

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
0.6.5	-Java-11-Python-3.7.4	GCCcore/8.3.0

trimAl

EVB, FEP and LIE simulator.

homepage: https://github.com/scapella/trimal

version	toolchain
1.4.1	GCC/8.2.0-2.31.1

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
0.39	-Java-11	system

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	versionsuffix	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
2.8.5	-Java-11	GCC/8.3.0
2.9.1	-Python-2.7.16	foss/2019b
2.9.1	-Python-3.7.4	foss/2019b
2.10.0	-Python-3.7.4	foss/2019b

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

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

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

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

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

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

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

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

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

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

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

U

UCLUST - UCX - udocker - UDUNITS - UFL - UMI-tools - umis - UNAFold - Unicycler - units - unixODBC - unrar - UnZip - UQTk - USEARCH - USPEX - utf8proc - util-linux

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

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

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

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

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

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

umis

Package for estimating UMI counts in Transcript Tag Counting data.

homepage: https://github.com/vals/umis

version	toolchain
1.0.3	intel/2019a

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

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

units

GNU Units converts quantities expressed in various systems of measurement to their equivalents in other systems of measurement. Like many similar programs, it can handle multiplicative scale changes. It can also handle nonlinear conversions such as Fahrenheit to Celsius or wire gauge, and it can convert from and to sums of units, such as converting between meters and feet plus inches.

homepage: https://www.gnu.org/software/units/

version	toolchain
2.19	GCCcore/8.2.0

unixODBC

unixODBC provides a uniform interface between application and database driver

homepage: https://www.unixodbc.org

version	toolchain
2.3.7	foss/2018b

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

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, GCCcore/8.3.0

UQTk

The UQ Toolkit (UQTk) is a collection of libraries and tools for the quantification of uncertainty in numerical model predictions.

homepage: https://www.sandia.gov/UQToolkit/

version	versionsuffix	toolchain
3.1.0	-Python-3.7.4	intel/2019b

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

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

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

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

V

V8 - Valgrind - Vampir - VarDict - VariantMetaCaller - VarScan - vartools - VASP - VAtools - VCF-kit - vcfnp - VCFtools - VEGAS - Velvet - VEP - verifyBamID - VERSE - ViennaRNA - Vim - VirSorter - VirtualGL - VMD - Voro++ - vsc-base - vsc-install - vsc-mympirun - vsc-mympirun-scoop - vsc-processcontrol - VSEARCH - vt - VTK - VTune - VV - VXL

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

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

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

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

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

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

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

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

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

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

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

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		GCC/8.3.0
0.1.16	-Perl-5.28.0	foss/2018b, intel/2018b

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

Velvet

Sequence assembler for very short reads

homepage: http://www.ebi.ac.uk/~zerbino/velvet/

version	versionsuffix	toolchain
1.2.10	-mt-kmer_191	GCC/8.3.0, foss/2018a, foss/2018b
1.2.10	-mt-kmer_37	intel/2017a

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

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

VERSE

A versatile and efficient RNA-Seq read counting tool

homepage: https://github.com/qinzhu/VERSE

version	toolchain
0.1.5	foss/2016b

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

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

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

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

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

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, foss/2019b, intel/2016a, intel/2019b

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

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

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

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

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

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

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

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

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

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

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

W

Wannier90 - WannierTools - wcwidth - WebKitGTK+ - WebSocket++ - WEKA - wget - wheel - WIEN2k - WildMagic - Winnowmap - WISExome - wkhtmltopdf - worker - WPS - WRF - WRF-Fire - wrf-python - wxPropertyGrid - wxPython - wxWidgets

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

WannierTools

an open-source software package for novel topological materials

homepage: http://www.wanniertools.com/

version	toolchain
2.3.0	intel/2018a

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

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

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

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

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, GCCcore/8.3.0

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

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

WildMagic

Wild Magic 5.17

homepage: https://www.geometrictools.com/index.html

version	toolchain
5.17	foss/2018b

Winnowmap

Winnowmap is a long-read mapping algorithm, and a result of our exploration into superior minimizer sampling techniques.

homepage: https://github.com/marbl/Winnowmap

version	toolchain
1.0	GCC/8.3.0

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

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

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

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

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

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

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

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

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

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

X

X11 - x264 - x265 - xarray - xbitmaps - xcb-proto - xcb-util - xcb-util-image - xcb-util-keysyms - xcb-util-renderutil - xcb-util-wm - xCell - XCfun - XCrySDen - Xerces-C++ - xextproto - xf86vidmodeproto - XGBoost - xineramaproto - XKeyboardConfig - XMDS2 - Xmipp - XML-LibXML - XML-Parser - xmlf90 - XMLSec - XMLStarlet - xonsh - xorg-macros - xprop - xproto - XSD - XTandem - xtb - xtrans - XZ

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

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

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

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
0.15.1	-Python-3.7.4	foss/2019b, intel/2019b

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

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

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

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

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

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

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

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

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

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
1.6.2	foss/2019b, intel/2019b

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

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

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

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
0.90	-Python-3.7.4	foss/2019b
20171120	-Java-1.8.0_152	intel/2017b

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

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

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

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

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

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

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
1.5.4	iccifort/2019.5.281

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

XMLStarlet

Command line XML tool

homepage: http://xmlstar.sourceforge.net

version	toolchain
1.6.1	GCCcore/6.4.0, foss/2016a

xonsh

Xonsh is a Python-ish, BASHwards-looking shell language and command prompt.

homepage: http://xon.sh/

version	toolchain
0.3.2	intel/2016a

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

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

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

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

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

xtb

xtb - An extended tight-binding semi-empirical program package.

homepage: https://xtb-docs.readthedocs.io

version	versionsuffix	toolchain
6.2.2-hotfix	-Python-3.6.3	intel/2017b
6.2.3		foss/2019b

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

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

Y

Yade - yaff - Yambo - YAPS - Yasm - YAXT

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

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	foss/2019b, intel/2019b

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

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

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

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

Z

zarr - ZeroMQ - zingeR - Zip - zlib - zlibbioc - ZPAQ - zsh - zstd

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

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

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

Zip

Zip is a compression and file packaging/archive utility. Although highly compatible both with PKWARE’s PKZIP and PKUNZIP utilities for MS-DOS and with Info-ZIP’s own UnZip, our primary objectives have been portability and other-than-MSDOS functionality

homepage: http://www.info-zip.org/Zip.html

version	toolchain
3.0	GCCcore/8.2.0, GCCcore/8.3.0

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/9.3.0, GCCcore/system, gimkl/2017a, system

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

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

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

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