From a4717da7b73ca2b2b6d53e2e930a87aa30a1bcb9 Mon Sep 17 00:00:00 2001
From: Nate Coraor <nate@bx.psu.edu>
Date: Sun, 27 Jan 2019 19:03:40 -0500
Subject: [PATCH] Add dependency_resolvers_conf.xml

---
 tasks/main.yml                             |  1 +
 templates/dependency_resolvers_conf.xml.j2 | 53 ++++++++++++++++++++++
 2 files changed, 54 insertions(+)
 create mode 100644 templates/dependency_resolvers_conf.xml.j2

diff --git a/tasks/main.yml b/tasks/main.yml
index 57227b8..d920783 100644
--- a/tasks/main.yml
+++ b/tasks/main.yml
@@ -60,3 +60,4 @@
     - server.ini
     - local_env.sh
     - job_metrics_conf.xml
+    - dependency_resolvers_conf.xml
diff --git a/templates/dependency_resolvers_conf.xml.j2 b/templates/dependency_resolvers_conf.xml.j2
new file mode 100644
index 0000000..f111e53
--- /dev/null
+++ b/templates/dependency_resolvers_conf.xml.j2
@@ -0,0 +1,53 @@
+<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>