Easystack files

This documentation covers aspects of specifying a software stack to install with Easybuild with easystack files.

Note: this is an experimental feature. Some of the mentioned functionality may be subject to change or be prone to errors.

The basics

Easystack files describe an entire software stack, and can be used to specify to EasyBuild what to install.

Usage

To build software with Easystack, type:

eb --easystack example.yaml --experimental

where example.yaml is the file with specifications that you just created (more about this in the next section).

Structure of an easystack file

Easystack files are written in YAML syntax.

General options, which should be applied to each software (for example robot), are defined at the top of the file.

Afterwards, particular software specifications follow.

It is mandatory to specify basic software-related keywords: software name, toolchains and versions.

  • software name: Name of the software.
  • toolchains: Names and versions of compiler Toolchains.
  • versions: Versions of software. If multiple entries are provided, EasyBuild will install all of them.

Can be in form of a list or consecutive line entries (see example).

General structure of YAML-formatted easystack:

software:
  <software_name>:
    toolchains:
      <toolchain name and version>:
          <software_version>:
            versionsuffix: '<-example>'

Example of YAML-formatted easystack:

software:
  Bioconductor:
    toolchains:
      foss-2020a:
        versions:
          3.11:
  EasyBuild:
    toolchains:
      SYSTEM:
        versions: [4.3.1]
  GROMACS:
    toolchains:
      foss-2020a:
        versions:
          2020.1:
          2020.3:
      fosscuda-2020a:
        versions: [2020.1]
  OpenFOAM:
    toolchains:
      foss-2020a:
        versions: [8, v2006]
  R:
    toolchains:
      foss-2020a:
        versions: [4.0.0]

To install the software specified in this easystack file named ‘myeasystack.yaml’, run:

eb --easystack myeasystack.yaml

This is equivalent to running:

eb Bioconductor-3.11-foss-2020a.eb EasyBuild-4.3.1-SYSTEM.eb GROMACS-2020.1-foss-2020a.eb GROMACS-2020.3-foss-2020a.eb GROMACS-2020.1-fosscuda-2020a.eb OpenFOAM-8-foss-2020a.eb OpenFOAM-v2006-foss-2020a.eb R-4.0.0-foss-2020a.eb

To be developed

Optionally, more advanced keywords can be specified: easybuild_version, robot, from_pr, versionsuffix, include-labels, exclude-labels.

  • easybuild_version: if present, EasyBuild will check if the easystack file was intended for the current version of EasyBuild.
  • robot: enables dependency resolution; see Using the EasyBuild command line for more details.
  • from_pr: easyconfig files that are added or modified by a particular pull request to the easybuild-easyconfigs GitHub repository can be used (regardless of whether the pull request is merged or not). (see Integration with GitHub for more details).
  • versionsuffix: additional suffix for software version (placed after toolchain name)
  • include-labels: only include this software when EasyBuild is configured with one of the specified labels
  • exclude-labels: do not include this software when EasyBuild is configured with one of the specified labels