From d6865ac07d87161bd3bd59e8b3fde7016723ab02 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 21 Aug 2019 12:31:12 -0400 Subject: [PATCH] Fix some data_dir stuff in galaxy.config. --- lib/galaxy/config/__init__.py | 5 ++--- 1 file changed, 2 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py index 2f29ff4ec44..76edf070354 100644 --- a/lib/galaxy/config/__init__.py +++ b/lib/galaxy/config/__init__.py @@ -359,7 +359,6 @@ class GalaxyAppConfiguration(BaseAppConfiguration): self.template_path = resolve_path(kwargs.get("template_path", "templates"), self.root) self.template_cache = resolve_path(kwargs.get("template_cache_path", "compiled_templates"), self.data_dir) self.job_queue_cleanup_interval = int(kwargs.get("job_queue_cleanup_interval", "5")) - self.cluster_files_directory = os.path.abspath(kwargs.get("cluster_files_directory", "database/pbs")) self.cluster_files_directory = os.path.abspath(resolve_path(kwargs.get("cluster_files_directory", "pbs"), self.data_dir)) # Fall back to legacy job_working_directory config variable if set. @@ -376,7 +375,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration): # should probably drop the backward compatiblity to save the path check. self.container_image_cache_path = resolve_path(kwargs.get("container_image_cache_path", "container_images"), self.data_dir) if not os.path.exists(self.container_image_cache_path): - self.container_image_cache_path = self.resolve_path(kwargs.get("container_image_cache_path", "database/container_cache")) + self.container_image_cache_path = resolve_path(kwargs.get("container_image_cache_path", "container_cache"), self.data_dir) self.outputs_to_working_directory = string_as_bool(kwargs.get('outputs_to_working_directory', False)) self.output_size_limit = int(kwargs.get('output_size_limit', 0)) self.retry_job_output_collection = int(kwargs.get('retry_job_output_collection', 0)) @@ -580,7 +579,7 @@ class GalaxyAppConfiguration(BaseAppConfiguration): self.nginx_upload_store = os.path.abspath(self.nginx_upload_store) self.object_store = kwargs.get('object_store', 'disk') self.object_store_check_old_style = string_as_bool(kwargs.get('object_store_check_old_style', False)) - self.object_store_cache_path = resolve_path(kwargs.get("object_store_cache_path", "database/object_store_cache"), self.data_dir) + self.object_store_cache_path = resolve_path(kwargs.get("object_store_cache_path", "object_store_cache"), self.data_dir) self.object_store_store_by = kwargs.get("object_store_store_by", "id") # Handle AWS-specific config options for backward compatibility