Merge pull request galaxyproject#2438 from ThomasWollmann/dev

fixed $defaults according to galaxyproject#2430

lib/galaxy/config.py

@@ -822,10 +822,11 @@ def _configure_toolbox( self ):
         galaxy_root_dir = os.path.abspath(self.config.root)
         file_path = os.path.abspath(getattr(self.config, "file_path"))
         app_info = containers.AppInfo(
-            galaxy_root_dir,
+            galaxy_root_dir=galaxy_root_dir,
             default_file_path=file_path,
             outputs_to_working_directory=self.config.outputs_to_working_directory,
             container_image_cache_path=self.config.container_image_cache_path,
+            library_import_dir=self.config.library_import_dir
         )
         self.container_finder = containers.ContainerFinder(app_info)
 

lib/galaxy/tools/deps/containers.py

@@ -152,12 +152,14 @@ def __init__(
         default_file_path=None,
         outputs_to_working_directory=False,
         container_image_cache_path=None,
+        library_import_dir=None
     ):
         self.galaxy_root_dir = galaxy_root_dir
         self.default_file_path = default_file_path
         # TODO: Vary default value for docker_volumes based on this...
         self.outputs_to_working_directory = outputs_to_working_directory
         self.container_image_cache_path = container_image_cache_path
+        self.library_import_dir = library_import_dir
 
 
 class ToolInfo(object):
@@ -295,6 +297,7 @@ def add_var(name, value):
         add_var("tool_directory", self.job_info.tool_directory)
         add_var("galaxy_root", self.app_info.galaxy_root_dir)
         add_var("default_file_path", self.app_info.default_file_path)
+        add_var("library_import_dir", self.app_info.library_import_dir)
 
         if self.job_info.job_directory:
             # We have a job directory, so everything needed (excluding index
@@ -307,6 +310,9 @@ def add_var(name, value):
         else:
             defaults = "$galaxy_root:ro,$tool_directory:ro,$working_directory:rw,$default_file_path:rw"
 
+        if self.app_info.library_import_dir:
+            defaults += ",$library_import_dir:ro"
+
         # Define $defaults that can easily be extended with external library and
         # index data without deployer worrying about above details.
         variables["defaults"] = string.Template(defaults).safe_substitute(variables)