Mercurial > repos > iuc > data_manager_gemini_downloader
view data_manager/data_manager_gemini_download.py @ 0:7848037cb701 draft default tip
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
author | iuc |
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date | Tue, 29 Dec 2015 10:58:29 -0500 |
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#!/usr/bin/env python import sys import os import json import shlex import datetime import subprocess 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'] ) ret = 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()