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. There is a default dependency resolver configuration but administrators can provide their own configuration
dependency_resolvers_conf.xml configuration file in the Galaxy
The binding between tool XML and the tools they need to run is specified in the tool XML using requirements 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
The requirement turn into inputs to the dependency resolver. Each dependency resolver is thus given given one or two inputs: the name of the dependency to resolve and, in most cases, the version string of the dependency.
Default Dependency Resolvers¶
The default configuration of dependency resolvers is equivalent to the following
<dependency_resolvers> <!-- the default configuration, first look for dependencies installed from the toolshed --> <tool_shed_packages /> <!-- then look for env.sh files profile according to the "galaxy packages" schema --> <galaxy_packages /> <galaxy_packages versionless="true" /> <conda /> <conda versionless="true" /> </dependency_resolvers>
This default dependency resolver configuration contains three items. First, the tool shed dependency resolver is used, then the Galaxy packages dependency resolver is used, first looking for packages by name and version string and then finally looking for the package just by name. The default configuration thus prefers packages installed from the Galaxy Tool Shed, before trying to find a “Galaxy package” satisfying the specific version the dependency requires before finally falling back to looking for a Galaxy package with merely the correct name. 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.
Tool Shed Dependency Resolver¶
tool_shed_packages dependency resolver works with packages installed from the Galaxy Tool Shed. When 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 name,
owner (in the Tool Shed) and version string (amongst other things) and ultimately contains a file named
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.
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¶
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
bedtools version 2.20.1, the dependency resolver will look for a directory
If the Galaxy Package dependency resolver finds a
bin directory in this directory, it adds it to the
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. For example, this
env.sh uses Environment Modules
to setup the environment for
#!/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 ending in
default. For example
bedtools/default. 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
modules dependency resolver it is possible to use Environment Modules directory. This resolver
takes these parameters:
- path to Environment Modules’
- value used for MODULEPATH environment variable, used to locate modules
- whether to resolve tools using a version string or not (default: false)
- whether to use the
AvailModuleChecker(permissable values are “directory” or “avail”, default is “avail”)
- in the AvailModuleChecker prefetch module info with
module avail(default: true)
- 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
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
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
The``DirectoryModuleChecker`` looks for files or directories in the path specified by
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.
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 XML tag can be used to configure a conda dependency resolver. This resolver can be configured with the following options.
- The conda_prefix used to locate dependencies in (default:
- The conda executable to use, it will default to the one on the
PATH (if available) and then to
- whether to resolve tools using a version string or not (default: false)
- Pass debug flag to conda commands (default: false).
- conda channels to enable by default. See http://conda.pydata.org/docs/custom-channels.html for more information about channels. (default: iuc,bioconda,r,defaults,conda-forge).
- Set to True to instruct Galaxy to look for and install missing tool dependencies before each job runs. (default: False)
- Set to True to instruct Galaxy to install conda from the web automatically if it cannot find a local copy and conda_exec is not configured.