Dependency Resolvers in Galaxy

There are two parts to building a link between Galaxy and command line bioinformatics tools: the tool XML that specifies a mapping between the Galaxy web user interface and the tool command line and tool dependencies that specify how to source the actual packages that implement the tool’s commands. The final script that Galaxy submits to run a job uses includes commands, such as changes to the PATH environment variable, that are generated by dependency resolvers. These same dependency resolvers are used by the Galaxy administrative UI to display whether an installed tool’s dependencies have been installed on the Galaxy server, and to show how they will be resolved at job runtime. There is a default dependency resolver configuration but administrators can provide their own configuration using the dependency_resolvers_conf.xml configuration file in the Galaxy config/ directory.

The binding between tool XML and the tools they need to run is specified in the tool XML using <requirement> tags, for example

<requirement type="package" version="0.7.10.039ea20639">bwa</requirement>

In some cases these requirement tags can be specified without a version

<requirement type="package">bedtools</requirement>

These declared requirements are passed as inputs to the dependency resolver.

Default Dependency Resolvers

The default configuration of dependency resolvers is equivalent to the following dependency_resolvers_conf.xml

<dependency_resolvers>
  <tool_shed_packages />
  <galaxy_packages />
  <conda />
  <galaxy_packages versionless="true" />
  <conda versionless="true" />
</dependency_resolvers>

This default dependency resolver configuration contains five items:

  1. First, the Tool Shed dependency resolver is used, which resolves packages installed from the Galaxy Tool Shed using legacy tool_dependencies.xml files,
  2. then the Galaxy packages dependency resolver is checked for a package matching the requirement name and version,
  3. then the Conda dependency resolver is checked for a package matching the requirement name and version. If no versioned match can be found, it then moves on to searching for unversioned matches, that is,
  4. the Galaxy packages dependency resolver is checked for a package matching the required name only, and
  5. finally the Conda dependency resolver is checked for a package matching the required name only.

If any of the dependency resolvers succeeds a dependency resolution object is returned and no more resolvers are called. This dependency resolution object provides shell commands to prepend to the shell script that runs the tool.

This order can be thought of as a descending order of deliberation. Tool Shed dependencies must be declared next to the tool by the tool author and must be selected for installation at tool installation time - this requires specific actions by both the tool author and the deployer who installed the tools. The dependency is therefore expected to highly crafted to the individual tool. If Galaxy packages have been setup, the deployer of a Galaxy tool has purposely crafted tool dependency statements for a specific installation - this is slightly less deliberate than tool shed packages but such requirements are less likely to be incidentally resolved than Conda packages. Conda recipes are neither tied to tools or a specific installation and are maintained in Conda channels such as Bioconda.

So while tool shed packages are first - they are also somewhat deprecated. Maintaining Conda recipes makes it easier to describe software dependencies both inside of Galaxy and outside.

Tool Shed Dependency Resolver

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.

Galaxy Packages Dependency Resolver

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 envh.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.

Environment Modules Dependency Resolver

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.

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.

Homebrew Dependency Resolver

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

Brew Tool Shed Package Resolver

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.

Conda Dependency Resolver

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 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,bioconda,r,defaults,conda-forge. This order should be consistent with 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+.