Merge pull request #17596 from bernt-matthias/data_manager_data_path

Automatically bind `galaxy_data_manager_data_path` in containers
galaxyproject · May 8, 2024 · 890a47b · 890a47b
2 parents 1bb139a + 8045855
commit 890a47b
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Showing 3 changed files with 6 additions and 0 deletions.
diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py
@@ -312,6 +312,7 @@ def _configure_toolbox(self):
             galaxy_root_dir=galaxy_root_dir,
             default_file_path=file_path,
             tool_data_path=self.config.tool_data_path,
+            galaxy_data_manager_data_path=self.config.galaxy_data_manager_data_path,
             shed_tool_data_path=self.config.shed_tool_data_path,
             outputs_to_working_directory=self.config.outputs_to_working_directory,
             container_image_cache_path=self.config.container_image_cache_path,

diff --git a/lib/galaxy/tool_util/deps/container_classes.py b/lib/galaxy/tool_util/deps/container_classes.py
@@ -338,6 +338,7 @@ def add_var(name, value):
         add_var("default_file_path", self.app_info.default_file_path)
         add_var("library_import_dir", self.app_info.library_import_dir)
         add_var("tool_data_path", self.app_info.tool_data_path)
+        add_var("galaxy_data_manager_data_path", self.app_info.galaxy_data_manager_data_path)
         add_var("shed_tool_data_path", self.app_info.shed_tool_data_path)
 
         if self.job_info.job_directory and self.job_info.job_directory_type == "pulsar":
@@ -376,6 +377,8 @@ def add_var(name, value):
             defaults += ",$library_import_dir:default_ro"
         if self.app_info.tool_data_path:
             defaults += ",$tool_data_path:default_ro"
+        if self.app_info.galaxy_data_manager_data_path:
+            defaults += ",$galaxy_data_manager_data_path:default_ro"
         if self.app_info.shed_tool_data_path:
             defaults += ",$shed_tool_data_path:default_ro"
 

diff --git a/lib/galaxy/tool_util/deps/dependencies.py b/lib/galaxy/tool_util/deps/dependencies.py
@@ -21,6 +21,7 @@ def __init__(
         galaxy_root_dir: Optional[str] = None,
         default_file_path: Optional[str] = None,
         tool_data_path: Optional[str] = None,
+        galaxy_data_manager_data_path: Optional[str] = None,
         shed_tool_data_path: Optional[str] = None,
         outputs_to_working_directory: bool = False,
         container_image_cache_path: Optional[str] = None,
@@ -35,6 +36,7 @@ def __init__(
         self.galaxy_root_dir = galaxy_root_dir
         self.default_file_path = default_file_path
         self.tool_data_path = tool_data_path
+        self.galaxy_data_manager_data_path = galaxy_data_manager_data_path
         self.shed_tool_data_path = shed_tool_data_path
         # TODO: Vary default value for docker_volumes based on this...
         self.outputs_to_working_directory = outputs_to_working_directory