From ad9686d136729d73e90490870b4fa799a4ea839f Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Fri, 13 Mar 2015 15:56:10 -0400 Subject: [PATCH 1/2] galaxy.metadata symlink so running jobs do not fail. --- lib/galaxy/metadata | 1 + 1 file changed, 1 insertion(+) create mode 120000 lib/galaxy/metadata diff --git a/lib/galaxy/metadata b/lib/galaxy/metadata new file mode 120000 index 00000000000..5eecd174bbb --- /dev/null +++ b/lib/galaxy/metadata @@ -0,0 +1 @@ +../galaxy_ext/metadata \ No newline at end of file From 710dfcf9f9368ede3882993bac5674cc6298b5ce Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Mon, 16 Mar 2015 10:05:37 -0400 Subject: [PATCH 2/2] In the metadata tool action, ensure job_working_directory exists before trying to get its path. Otherwise, hierarchical/distributed object stores will be broken. --- lib/galaxy/tools/actions/metadata.py | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/galaxy/tools/actions/metadata.py b/lib/galaxy/tools/actions/metadata.py index eb772f5f80d..6acea06e90a 100644 --- a/lib/galaxy/tools/actions/metadata.py +++ b/lib/galaxy/tools/actions/metadata.py @@ -70,6 +70,7 @@ class SetMetadataToolAction( ToolAction ): # Store original dataset state, so we can restore it. A separate table might be better (no chance of 'losing' the original state)? incoming[ '__ORIGINAL_DATASET_STATE__' ] = dataset.state input_paths = [DatasetPath( dataset.id, real_path=dataset.file_name, mutable=False )] + app.object_store.create(job, base_dir='job_work', dir_only=True, extra_dir=str(job.id)) job_working_dir = app.object_store.get_filename(job, base_dir='job_work', dir_only=True, extra_dir=str(job.id)) external_metadata_wrapper = JobExternalOutputMetadataWrapper( job ) cmd_line = external_metadata_wrapper.setup_external_metadata( dataset,