Galaxy Main ToolShed

Simple Repository Dependencies

Simple repository dependencies are repository dependency definitions that define relationships from the dependent repository (the one containing the repository_dependencies.xml file) to any number of additional, separate required repositories. These definitions are categorized as "simple" because the the contents of the related repositories is not considered. These kinds of relationships include 2 features:

  • they enable installation of multiple related repositories
  • The status of the dependent repository will display the status of its repository dependencies

An example of a repository that contains a simple repository dependency definition is the emboss_5 repository in the main Galaxy ToolShed. The emboss_datatypes repository defined as a required repository with the inclusion of a file named repository_dependencies.xml in the emboss_5 repository. Here are the contents of the repository_dependencies.xml file contained within the emboss_5 repository.

<?xml version="1.0"?>
<repositories description="Emboss 5 requires the Galaxy applicable data formats used by Emboss tools.">
     <repository toolshed="http://toolshed.g2.bx.psu.edu" name="emboss_datatypes" owner="devteam" changeset_revision="a89163f31369" />
</repositories>

The <repositories> tag set can contain any number of <repository> tags, each of which will define a dependency relationship to a specific repository name/owner/changeset revision combination within the ToolShed.

========================================================================================= Important note: the <repository> tag requires 2 of the 4 attributes shown above (name and owner are required), while the other 2 (toolshed and changeset_revision) are optional. If the toolshed attribute is not defined, the attribute will be set as the local ToolShed. If the changeset_revision is not defined, the attribute will be defined as the latest installable changeset_revision of the repository within the ToolShed defined by name and owner. In either case, the repository_dependencies.xml file will be automatically altered to have these attributes included in the tag with these default values. This automatic alteration will take place before the changeset containing the repository_dependencies.xml file is committed to the repository in the ToolShed. A 5th attribute named prior_installation_required is optional as well. If defined, the value should always be "True". When used, this attribute ensures that the required repository will be installed prior to it's dependent repository. See the Supported tags sets for the tool_dependencies.xml file section of the ToolShed wiki for details about all of the supported tool dependency definition tag sets. =========================================================================================