Mercurial > repos > chrisw > data_manager_monorail_index_fetcher
changeset 10:7d7328ce424b draft
Uploaded
author | chrisw |
---|---|
date | Wed, 13 Nov 2019 21:02:28 +0000 |
parents | 79f33bace3da |
children | 11daa95fdc3e |
files | data_manager_monorail_index/data_manager/data_manager.py data_manager_monorail_index/data_manager_conf.xml |
diffstat | 2 files changed, 3 insertions(+), 2 deletions(-) [+] |
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--- a/data_manager_monorail_index/data_manager/data_manager.py Wed Nov 13 20:56:31 2019 +0000 +++ b/data_manager_monorail_index/data_manager/data_manager.py Wed Nov 13 21:02:28 2019 +0000 @@ -27,6 +27,7 @@ target_directory = params['output_data'][0]['extra_files_path'] #data_manager_entry['path'] = params['output_data'][0]['extra_files_path'] data_manager_entry['path'] = target_directory + data_manager_entry['name'] = ref #data_manager_entry['exons_path'] = data_manager_entry['path'] + os.sep + 'gtf' + os.sep + 'exons.bed' data_manager_json = dict(data_tables={'monorail_index': [data_manager_entry]}) file(args.output, 'wb').write(json.dumps(data_manager_json))
--- a/data_manager_monorail_index/data_manager_conf.xml Wed Nov 13 20:56:31 2019 +0000 +++ b/data_manager_monorail_index/data_manager_conf.xml Wed Nov 13 21:02:28 2019 +0000 @@ -8,9 +8,9 @@ <column name="path" output_ref="out_file"> <move relative_symlinks="True" type="directory"> <!-- no need to set source, gets taken from out_dir.extra_files_path --> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/</target> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">${dbkey}/mri/${value}</target> </move> - <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/{$dbkey}/${path}</value_translation> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/{$dbkey}/mri/${value}/${path}</value_translation> <value_translation type="function">abspath</value_translation> </column> </output>