Galaxy Main Tool Shed

Complex Repository Dependencies

Complex repository dependencies allow many Tool Shed repository installations into a single Galaxy instance where any number of the contained tools across installed repositories can all reference a single installation of a specific tool dependency package (e.g. bwa version 0.5.9).

Describing how this works is tricky, so let's see if we can state it in a way that can be understood: tool dependency definitions that contain repository dependency definitions define a relationship to a tool dependency that will be installed using the instructions in the required repository's tool_dependencies.xml file, where the relationship to the required repository is defined by the contained repository dependency definition. Hmmm...okay, let's try to clarify this a bit...

To demonstrate how this works, we'll refer to 2 repositories in the test Galaxy Tool Shed: bwa_059 and complex_repository_dependency_on_bwa_059.

The bwa_059 repository has type Tool dependency definition and contains only a single file named tool_dependencies.xml which looks like the following. This definition will download and compile version 0.5.9 of the bwa package.

<?xml version="1.0"?>
    <package name="bwa" version="0.5.9">
        <install version="1.0">
                <action type="download_by_url"></action>
                <action type="shell_command">make clean</action>
                <action type="shell_command">make</action>
                <action type="move_file">
                <action type="set_environment">
                    <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
Compiling BWA requires zlib and libpthread to be present on your system.

To demonstrate how the bwa_059 repository can be used, let's take a look at the tool_dependencies.xml file contained in the complex_repository_dependency_on_bwa_059 repository, which looks like the following.

<?xml version="1.0"?>
    <package name="bwa" version="0.5.9">
        <repository toolshed="" name="bwa_059" owner="greg" changeset_revision="a347750db1d1" />

The above tool dependency definition is associated with the entry in the <requirements> tag set defined in the bwa_wrapper.xml Galaxy tool configuration file contained in the same repository. The bwa_wrapper.xml <requirements> tag set looks like the following. Notice that the type package, version 0.5.9 and name bwa match the definition in the above tool_dependencies.xml file.

    <requirement type="package" version="0.5.9">bwa</requirement>

Visiting the repository's main page displays various containers. There are two dependencies defined for this repository, both of which are defined in the simple tool_dependencies.xml file above. The repository dependency on revision a347750db1d1 of the repository named bwa_059 owned by greg is defined by the repository tag, while the tool dependency on version 0.5.9 of the bwa package is defined by the <package> tag set.

For more technical details on this XML file, see the supported tool_dependencies.xml tag sets.