Mercurial > repos > chrisw > data_manager_monorail_index_fetcher
changeset 19:e7d440a3b439 draft
Uploaded
| author | chrisw |
|---|---|
| date | Thu, 14 Nov 2019 02:23:06 +0000 |
| parents | 402c6528fb6f |
| children | 166451f0ac6a |
| files | data_manager_monorail_index/data_manager/data_manager.py data_manager_monorail_index/data_manager/download_and_extract_monorail_index.sh |
| diffstat | 2 files changed, 4 insertions(+), 4 deletions(-) [+] |
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--- a/data_manager_monorail_index/data_manager/data_manager.py Thu Nov 14 02:12:39 2019 +0000 +++ b/data_manager_monorail_index/data_manager/data_manager.py Thu Nov 14 02:23:06 2019 +0000 @@ -11,7 +11,7 @@ parser = argparse.ArgumentParser(description='Create data manager json.') parser.add_argument('--config', dest='config', action='store', help='JSON filename') -parser.add_argument('--name', dest='name', action='store', default=None, help='Data table entry unique ID') +#parser.add_argument('--name', dest='name', action='store', default=None, help='Data table entry unique ID') parser.add_argument('--url', dest='url', action='store', help='Monorail Indexes Base URL', default="http://snaptron.cs.jhu.edu/data/monorail/1.0.0/ath10") parser.add_argument('--subdir', dest='subdir', action='store', help='subdirectory where the indexes are temporarily downloaded to') #parser.add_argument('--version', dest='version', action='store', help='Version of Monorail as a whole (not a particular index/program)') @@ -33,7 +33,7 @@ #data_manager_entry['path'] = params['output_data'][0]['extra_files_path'] data_manager_entry['path'] = args.subdir data_manager_entry['exons_path'] = args.subdir - data_manager_entry['version'] = args.version + data_manager_entry['version'] = version #data_manager_entry['exons_path'] = data_manager_entry['path'] + os.sep + 'gtf' + os.sep + 'exons.bed' data_manager_json = {'data_tables':{'monorail_index': [data_manager_entry]}} file(args.output, 'w').write(json.dumps(data_manager_json))
--- a/data_manager_monorail_index/data_manager/download_and_extract_monorail_index.sh Thu Nov 14 02:12:39 2019 +0000 +++ b/data_manager_monorail_index/data_manager/download_and_extract_monorail_index.sh Thu Nov 14 02:23:06 2019 +0000 @@ -1,11 +1,11 @@ #!/bin/bash target_dir=$1 -#e.g. http://snaptron.cs.jhu.edu/data/monorail/ath10 or http://snaptron.cs.jhu.edu/data/monorail/hg38 +#e.g. http://snaptron.cs.jhu.edu/data/monorail/1.0.0/ath10 or http://snaptron.cs.jhu.edu/data/monorail/1.0.0/hg38 ref=$2 if [[ -z $ref ]]; then - ref='http://snaptron.cs.jhu.edu/data/monorail/ath10' + ref='http://snaptron.cs.jhu.edu/data/monorail/1.0.0/ath10' fi url=$ref