Mercurial > repos > iuc > data_manager_gemini_database_downloader
view data_manager/data_manager_gemini_download.py @ 3:172815da3d41 draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 8652f36a3a3838dca989426961561e81432acf4f
author | iuc |
---|---|
date | Tue, 04 Apr 2017 18:09:05 -0400 |
parents | 345412d58d75 |
children | fe5a9a7d95b0 |
line wrap: on
line source
#!/usr/bin/env python import datetime import json import os import subprocess import sys def main(): today = datetime.date.today() params = json.loads( open( sys.argv[1] ).read() ) target_directory = params[ 'output_data' ][0]['extra_files_path'] os.mkdir( target_directory ) cmd = "gemini --annotation-dir %s update --dataonly %s %s" % (target_directory, params['param_dict']['gerp_bp'], params['param_dict']['cadd'] ) subprocess.check_call( cmd, shell=True ) data_manager_dict = { 'data_tables': { 'gemini_databases': [ {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } ] } } # save info to json file with open( sys.argv[1], 'wb' ) as out: out.write( json.dumps( data_manager_dict ) ) if __name__ == "__main__": main()