Merge pull request #132 from mapa17/Fix_conda_auto_install

Fixing conda_auto resolving

dependency_resolvers_conf.xml.sample

+<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
+   	auto_install: Set to True to instruct Galaxy to look for and install missing tool dependencies before each job runs. (default: False)
+   	auto_init: Set to True to instruct Galaxy to install conda from the web automatically if it cannot find a local copy and conda_exec is not configured. 
+    	-->
+	<conda auto_install="True" auto_init="True"/>
+
+
+        <!-- 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" />
+
+        <!-- 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
+-->
+</dependency_resolvers>

pulsar/core.py

@@ -127,8 +127,8 @@ class PulsarApp(object):
         conda_config = {}
         for key, value in conf.items():
             if key.startswith("conda_"):
-                conda_config[key] = value
-        self.dependency_manager = DependencyManager(dependencies_dir, resolvers_config_file, **conda_config)
+                conda_config[key[len('conda_'):]] = value
+        self.dependency_manager = DependencyManager(dependencies_dir, resolvers_config_file, app_config=conda_config)
 
     def __setup_job_metrics(self, conf):
         job_metrics = conf.get("job_metrics", None)