LMOD Dependency resolver - Default mapping file

If a lmod_modules_mapping.yml file exists in the config folder then it will be taken into consideration automatically to map Galaxy requirements to LMOD modules.

config/dependency_resolvers_conf.xml.sample

@@ -20,12 +20,13 @@
   * 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 the 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: None
+  * 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
+   - 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 />

config/lmod_modules_mapping.yml.sample

@@ -0,0 +1,47 @@
+# This is an example mapping file for the LMOD Dependency resolver (in YAML format)
+#
+# The goal of this file is to map tool's requirements to existing LMOD modules available on your system
+# Of course, if the name of a requirement and the name of a module match perfectly, there is no need to map them together through this mapping file.
+#
+# This is a sample file so the first thing to do to activate the mapping system is to create a copy of this file called "lmod_modules_mapping.yml".
+# The Lmod dependency resolver is programmed to search and use this YAML file automatically if it exists in the "config" folder of your Galaxy instance.
+# Alternatively, you can also use the "mapping_files" attribute of the <lmod /> resolver in the dependency_resolvers_conf.xml file to specify a custom mapping file
+#
+# Example 1:
+#
+# Let's say that one of the wrapper installed on your Galaxy instance has the following requirement:
+#
+#	<requirements>
+#		<requirement type="package" version="1.5.0">PIPITS</requirement>
+#	</requirements>
+#
+# But unfortunately, the name of the corresponding module file on your system is "pipits_pipeline/1.5.0"
+#
+# Then, to make Galaxy load/unload the appropriate module, you just have to add the following lines (without to the #) to the "lmod_modules_mapping.yml" file:
+#
+#- from:
+#    name: PIPITS
+#    version: 1.5.0
+#  to:
+#    name: pipits_pipeline
+#    version: 1.5.0.6
+#
+#
+# Example 2:
+#
+# The requirements section specify a requirement on the PIPITS tool but do not ask for a specific version of it:
+#
+#	<requirements>
+#		<requirement type="package">PIPITS</requirement>
+#	</requirements>
+#
+# Although, there is no version required you may want to force the loading of a version that is known to run well on your system.
+#
+# In that case you can add the following lines to the "lmod_modules_mapping.yml" file:
+#
+#- from:
+#    name: PIPITS
+#    unversioned: true
+#  to:
+#    name: pipits_pipeline
+#    version: 1.4.0

lib/galaxy/tools/deps/resolvers/lmod.py

@@ -25,6 +25,7 @@ log = logging.getLogger(__name__)
 DEFAULT_LMOD_PATH = getenv('LMOD_CMD')
 DEFAULT_SETTARG_PATH = getenv('LMOD_SETTARG_CMD')
 DEFAULT_MODULEPATH = getenv('MODULEPATH')
+DEFAULT_MAPPING_FILE = 'config/lmod_modules_mapping.yml'
 INVALID_LMOD_PATH_MSG = "The following LMOD executable could not be found: %s. Either your LMOD Dependency Resolver is misconfigured or LMOD is improperly installed on your system !"
 EMPTY_MODULEPATH_MSG = "No valid LMOD MODULEPATH defined ! Either your LMOD Dependency Resolver is misconfigured or LMOD is improperly installed on your system !"
 
@@ -35,13 +36,22 @@ class LmodDependencyResolver(DependencyResolver, MappableDependencyResolver):
     resolver_type = "lmod"
 
     def __init__(self, dependency_manager, **kwds):
+        # Mapping file management
+        self._set_default_mapping_file(kwds)
         self._setup_mapping(dependency_manager, **kwds)
+
+        # Other attributes
         self.versionless = _string_as_bool(kwds.get('versionless', 'false'))
         self.lmodexec = kwds.get('lmodexec', DEFAULT_LMOD_PATH)
         self.settargexec = kwds.get('settargexec', DEFAULT_SETTARG_PATH)
         self.modulepath = kwds.get('modulepath', DEFAULT_MODULEPATH)
         self.module_checker = AvailModuleChecker(self, self.modulepath)
 
+    def _set_default_mapping_file(self, resolver_attributes):
+        if not resolver_attributes.has_key('mapping_files'):
+            if exists(DEFAULT_MAPPING_FILE):
+                resolver_attributes['mapping_files'] = DEFAULT_MAPPING_FILE
+
     def resolve(self, requirement, **kwds):
         requirement = self._expand_mappings(requirement)
         name, version, type = requirement.name, requirement.version, requirement.type