annotate docker/dependency_resolvers_conf.xml @ 19:8503457bd0c4 draft

planemo upload for repository https://github.com/igg-molecular-biology-lab/pipe-t.git commit f98eba79c2036aa3e1b8f9048c0b1e61d4d87b60

<dependency_resolvers>
  <!-- the default configuration, first look for dependencies installed from the toolshed -->
  <tool_shed_packages />
  <!-- then look for env.sh files in directories according to the "galaxy packages" schema.
       These resolvers can take a base_path attribute to specify where to look for
       package definitions, but by default look in the directory specified by tool_dependency_dir
       in Galaxy's config/galaxy.ini -->
  <galaxy_packages />
  <!-- check whether the correct version has been installed via conda -->
  <conda />
  <!-- look for a "default" symlink pointing to a directory containing an
       env.sh file for the package in the "galaxy packages" schema -->
  <galaxy_packages versionless="true" />
  <!-- look for any version of the dependency installed via conda -->
  <conda versionless="true" />

  <!-- LMOD dependency resolver (For the LMOD environment modules system - https://github.com/TACC/Lmod) -->
  <!--
  The LMOD dependency resolver attributes are:
  * lmodexec - Path to the lmod executable on your system - Default: value of the "LMOD_CMD" environment variable
  * settargexec - Path to the settarg executable on your system - Default: value of the "LMOD_SETTARG_CMD" environment variable
  * modulepath - Path to the folder that contains the LMOD module files on your system - Default: value of the "MODULEPATH" environment variable
  * versionless - Set it to true to resolve a dependency based on its name only (the version number is ignored) - Default: false
  * mapping_files - Path to a Yaml configuration file that can be used to link tools requirements with existing LMOD modules - Default: config/lmod_modules_mapping.yml
  Important notes:
   - All the above attributes are optional
   - The value of the lmodexec attribute can't just be "module" because module is actually a bash function and not the real LMOD binary (see the result of the "type module" command)
   - The value of the modulepath attribute can also be a semicolon separated list of path
   - In versionless mode, only modules marked as Default will be listed by the "avail" command (The -d option is used)
   - If the config folder of your Galaxy instance contains a file called "lmod_modules_mapping.yml" (based on the lmod_modules_mapping.yml.sample file) it will be taken into consideration automatically
  -->
  <!--
  <lmod />
  <lmod versionless="true" />
  -->

  <!-- Example configuration of modules dependency resolver, uses Environment Modules -->
  <!--
  <modules modulecmd="/opt/Modules/3.2.9/bin/modulecmd" />
  <modules modulecmd="/opt/Modules/3.2.9/bin/modulecmd" versionless="true" default_indicator="default" />
  Attributes are:
  * modulecmd - path to modulecmd
  * versionless - default: false - whether to resolve tools using a version number or not
  * find_by - directory or avail - use the DirectoryModuleChecker or AvailModuleChecker
  * prefetch - default: true - in the AvailModuleChecker prefetch module info with 'module avail'
  * default_indicator - default: '(default)' - what indicate to the AvailModuleChecker that a module is the default version
  -->

  <!-- other resolvers
  <tool_shed_tap />
  <homebrew />
  -->
</dependency_resolvers>