annotate data_manager/data_manager_gemini_download.py @ 2:345412d58d75 draft

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_database_downloader commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4

#!/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()