Dependency Resolvers in Galaxy¶
There are two parts to building a link between Galaxy and command line bioinformatics tools: (1) the tool XML that
specifies a mapping between the Galaxy web user interface and the tool command line, and (2) system tool dependencies that
specify how to source the actual packages that implement the tool’s commands. The job script that Galaxy uses to run a job
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
The binding between tool XML and the system tools they need to run is specified in the tool XML using
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
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> <tool_shed_packages /> <galaxy_packages /> <conda /> <galaxy_packages versionless="true" /> <conda versionless="true" /> </dependency_resolvers>
This default dependency resolver configuration contains five items:
- First, the Tool Shed dependency resolver is used, which resolves packages installed from the Galaxy Tool Shed
- then the Galaxy packages dependency resolver is checked for a package matching the requirement name and version,
- 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,
- the Galaxy packages dependency resolver is checked for a package matching the required name only, and
- finally the Conda dependency resolver is checked for a package matching the required name only.
If any of the dependency resolvers succeed, 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 system 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 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¶
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¶
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.yml. 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.
A simple example might be to assume that a collection of bioinformatics software is manually installed in various
/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
#!/bin/sh export PATH=$PATH:/opt/biosoftware/bedtools/2.20.1/bin
As another example, this
env.sh uses Environment Modules
to setup the environment for
#!/bin/sh if [ -z "$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
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.
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:
- whether to use the
AvailModuleChecker(permissable values are
avail, default is
- in the AvailModuleChecker prefetch module info with
- 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
(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. 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¶
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.
- 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:
- Pass debug flag to conda commands (default:
- conda channels to enable by default. See
https://conda.io/docs/user-guide/tasks/manage-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
True, Galaxy will look for and install missing tool dependencies before running a job (default:
True, Galaxy will try to install Conda from the web automatically if it cannot find a local copy and
conda_execis not configured. This defaults to
Trueas of Galaxy 17.01.
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+.