Dependency Resolution

galaxy-lib includes a pluggable dependency resolution system that can be used to map software descriptions (such a Galaxy requirement tags or CWL tool SoftwareRequirement annotations) to shell command that inject these software requirements into a shell job.

This module for dependency resolution has been integrated with:

Dependency resolvers are configured from within a dependency resolvers configuration file (e.g. dependency_resolvers_conf.yml). This file can be either XML or YAML and must contain an ordered list of dependency resolvers to configure.

The dependency resolution system will attempt to walk through each requirement and find the first resolver that matches that requirement. The configuration corresponding to the default Galaxy resolution is discussed here and various CWL examples are worked through in the cwltool README here.

Below some of the command resolvers are discussed in detail and some of their options are described as well but no promise of completeness is made. Please consult the code for the latest options.

The Resolvers

Conda Dependency Resolver - conda

The conda directive can be used to configure a conda dependency resolver. This resolver can be configured with the following options.

For a very detailed discussion of Conda dependency resolution, check out the Galaxy Conda FAQ.

prefix
The conda_prefix used to locate dependencies in (default: <tool_dependency_dir>/_conda).
exec
The conda executable to use, it will default to the one on the PATH (if available) and then to <conda_prefix>/bin/conda.
versionless
whether to resolve tools using a version string or not (default: False).
debug
Pass debug flag to conda commands (default: False).
ensure_channels
conda channels to enable by default. See http://conda.pydata.org/docs/custom-channels.html for more information about channels. This defaults to iuc,conda-forge,bioconda,defaults. This order should be consistent with the Bioconda prescribed order if it includes bioconda.
auto_install
If True, Galaxy will look for and install missing tool dependencies before running a job (default: False).
auto_init
If True, Galaxy will try to install Conda from the web automatically if it cannot find a local copy and conda_exec is not configured. This defaults to True as of Galaxy 17.01.
copy_dependencies
If True, Galaxy will copy dependencies over instead of symbolically linking them when creating per job environments. This should be considered somewhat deprecated because Conda will do this as needed for newer versions of Conda - such as the version targeted with Galaxy 17.01+.
mapping_files
See a discussion of mapping files below.

Galaxy Packages Dependency Resolver - galaxy_packages

The galaxy_packages dependency resolver allows Galaxy admins to specify how Galaxy should load manually installed packages. This resolver can be configured either to use the version string or in versionless mode.

The Galaxy Packages dependency resolver takes a base_path argument that specifies the path under which it starts looking for the files it requires. The default value for this base_path is the tool_dependency_dir configured in Galaxy’s config/galaxy.ini. Below the base path, the Galaxy Packages resolver looks for directories named after tools, e.g. bedtools. As mentioned before, this resolver works in versioned and versionless mode. The default mode is versioned, where the dependency resolver looks for a directory named after the dependency’s version string. For example, if the Galaxy tool specifies that it needs bedtools version 2.20.1, the dependency resolver will look for a directory bedtools/2.20.1.

If the Galaxy Package dependency resolver finds a bin directory in this directory, it adds it to the PATH used by the scripts Galaxy uses to run tools. If, however, it finds an env.sh script, it sources this script before running the tool that requires this dependency. This can be used to set up the environment needed for the tool to run.

A simple example might be to assume that a collection of bioinformatics software is manually installed in various directories under /opt/biosoftware. In this case a <tool_dependency_dir>/bedtools/2.20.1/env.sh could be setup to add the corresponding bedtools installation to the Galaxy tool execution’s PATH.

#!/bin/sh

export PATH=$PATH:/opt/biosoftware/bedtools/2.20.1/bin

As another example, this env.sh uses Environment Modules to setup the environment for bedtools

#!/bin/sh

if [ -z "$MODULEPATH" ] ; then
  . /etc/profile.d/module.sh
fi

module add bedtools/bedtools-2.20.1

The Galaxy Package dependency resolver operates quite similarly when used in versionless module. Instead of looking for a directory named after a version, it looks for a directory symbolic link named default that links to a concrete version such as the 2.20.1 example above. For example if bedtools/default links to bedtools/2.20.1. It then looks for a bin subdirectory or env.sh and incorporates these in the tool script that finally gets run. This versionless (i.e. default) lookup is also used if the package requirement does not specify a version string.

The mapping_file parameter on can be set on the dependency resolution directive for the galaxy_packages dependency resolver. See a discussion of mapping files below for more information.

Environment Modules Dependency Resolver - modules

The example above used Environment Modules to set the PATH (and other settings) for bedtools. With the modules dependency resolver it is possible to use Environment Modules directory. This resolver takes these parameters:

modulecmd
path to Environment Modules’ modulecmd tool
modulepath
value used for MODULEPATH environment variable, used to locate modules
versionless
whether to resolve tools using a version string or not (default: false)
find_by
whether to use the DirectoryModuleChecker or AvailModuleChecker (permissable values are directory or avail, default is avail)
prefetch
in the AvailModuleChecker prefetch module info with module avail (default: true)
default_indicator
what indicate to the AvailModuleChecker that a module is the default version (default: (default)). Note that the first module found is considered the default when no version is used by the resolver, so the sort order of modules matters.
mapping_files
See a discussion of mapping files below.

The Environment Modules dependency resolver can work in two modes. The AvailModuleChecker searches the results of the module avail command for the name of the dependency. If it is configured in versionless mode, or is looking for a package with no version specified, it accepts any module whose name matches and is a bare word or the first module whose name matched. For this reason, the default version of the module should be the first one listed, something that can be achieved by tagging it with a word that appears first in sort order, for example the string (default) (yielding a module name like bedtools/(default)). So when looking for bedtools in versionless mode the search would match the first module called bedtools, and in versioned mode the search would only match if a module named bedtools/2.20.1 was present (assuming you’re looking for bedtools/2.20.1).

The``DirectoryModuleChecker`` looks for files or directories in the path specified by MODULEPATH or MODULESHOME that match the dependency being resolved. In versionless mode a match on simply the dependency name is needed, and in versioned mode a match on the dependency name and version string is needed.

If a module matches the dependency is found, code to executed modulecmd sh load with the name of the dependency is added to the script that is run to run the tool. E.g. modulecmd sh load bedtools. If version strings are being used, they’ll be used in the load command e.g. modulecmd sh load bwa/0.7.10.039ea20639.

LMOD Dependency Resolver - lmod

The LMOD dependency resolver closely mirrors the environment module dependency resolver but is optimized to target the LMOD module system.

The options available to this dependency resolver include:

versionless
whether to resolve tools using a version string or not (default is false).
lmodexec
Path to the lmod executable on your system (default the value of the LMOD_CMD environment variable).
settargexec
Path to the settarg executable on your system (default is the value of the LMOD_SETTARG_CMD environment variable)
modulepath
Path to the folder that contains the LMOD module files on your system (default is the value of the MODULEPATH environment variable)
mapping_files
See a discussion of mapping files below.

The LMOD dependency was implemented in Galaxy Pull Request #4489 by @arbernard.

Tool Shed Dependency Resolver - tool_shed_packages

Unlike the other dependency resolvers described here - this one is likely only useful from within Galaxy.

The tool_shed_packages dependency resolver works with explicit software packages installed from the Galaxy Tool Shed as described by legacy tool_dependencies.xml files. When such a package is installed from the Tool Shed it creates a directory structure under the directory that is specified as the tool_dependency_dir in Galaxy’s configuration. This directory structure contains references to the tool’s ID, owner (in the Tool Shed) and version string (amongst other things) and ultimately contains a file named env.sh that contains commands to make the dependency runnable. This is installed, along with the packaged tool, by the tool package and doesn’t require any configuration by the Galaxy administrator.

Tools installed from the Tool Shed may also install Conda recipes and most new best practice tools do this by default now.

The Tool Shed dependency resolver is not able to resolve package requirements that do not have a version string, like the bedtools example above.

Homebrew Dependency Resolver - homebrew

This dependency resolver uses homebrew packages to resolve requirements. It is highly experimental and undocumented.

Brew Tool Shed Package Resolver - shed_tap

This dependency resolver would resolve tool shed packages that had been auto converted to the tool shed. It is highly experimental, undocumented, and will almost certainy be removed from the code base.

Mapping Files

A few different dependency resolvers allow specification of a mapping_files parameter. If specified, these files describe rules to rewrite the abstract requirements from tools to locally available values on either the system or in a known package source such as Bioconda. Check out Galaxy Pull Request #3444 and Pull Request #3509 for implementation details.

The format of the mapping files is simple a YAML file with a flat list of “rules”. Each rule should specify a from condition describing the abstract requirements to map and a to value that describes how the requirement should be rewritten.

Consider the following CWL SoftwareRequirement and Galaxy requirement:

hints:
  SoftwareRequirement:
    packages:
    - package: 'random-lines'
      version:
      - '1.0'

<requirement type="package" version="1.0">random-lines</requirement>

Now imaging some galaxy_package or environment Module named randomLines fullfills this requirement and is configured with a version of 1.0.0-rc1. The following mapping rule would allow redirecting the corresponding resolver to target that package:

- from:
    name: randomLines
    version: 1.0.0-rc1
  to:
    name: random-lines
    version: '1.0'

If no version is specified, all versions will be targetted and the from value can simply the requirement name instead of a dictionary. To just target requirements without specified versions set unversioned: true in the requirement rule. For instance:

- from:
    name: package
    unversioned: true
  to:
    name: package
    version: 1.3.1

By default, Galaxy (not galaxy-lib) configures some mappings from Conda in the file default_conda_mapping.yml

Here are some examples from that file:

- from: R
  to: r-base
- from: blast+
  to: blast
- from:
    name: samtools
    unversioned: true
  to:
    name: samtools
    version: 1.3.1
- from:
    name: ucsc_tools
    unversioned: true
  to:
    name: ucsc_tools
    version: 332
- from:
    name: bedtools
    unversioned: true
  to:
    name: bedtools
    version: 2.26.0gx

Galaxy also sets up some default mapping files for both the conda and lmod dependency resolvers if the files config/local_conda_mapping.yml or config/lmod_modules_mapping.yml respectively are present in Galaxy.