Mercurial > repos > iuc > data_manager_gemini_database_downloader

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

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planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_database_downloader commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
author iuc
date Thu, 18 Feb 2016 08:49:06 -0500
parents fd9e9ac5ecb3
children 172815da3d41
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1:a580422f6f1d 2:345412d58d75
8 import subprocess 8 import subprocess
9 9
10 def main(): 10 def main():
11 11
12 today = datetime.date.today() 12 today = datetime.date.today()
13 gemini_root_dir = os.environ['GEMINI_ROOT_DIR']
14 params = json.loads( open( sys.argv[1] ).read() ) 13 params = json.loads( open( sys.argv[1] ).read() )
15 target_directory = params[ 'output_data' ][0]['extra_files_path'] 14 target_directory = params[ 'output_data' ][0]['extra_files_path']
16 os.mkdir( target_directory ) 15 os.mkdir( target_directory )
17 gemini_exec = os.path.join( gemini_root_dir, 'gemini', 'gemini', 'install-data.py' ) 16 cmd = "gemini --annotation-dir %s update --dataonly %s %s" % (target_directory, params['param_dict']['gerp_bp'], params['param_dict']['cadd'] )
18 cmd = gemini_exec + " %s %s" % (' '.join( [params['param_dict']['gerp_bp'], params['param_dict']['cadd']] ), target_directory)
19 #cmd = gemini_exec + " --help > %s/foo.txt" % target_directory
20 ret = subprocess.check_call( cmd, shell=True ) 17 ret = subprocess.check_call( cmd, shell=True )
21 data_manager_dict = { 18 data_manager_dict = {
22 'data_tables': 19 'data_tables':
23 {'gemini_databases': [ 20 {'gemini_databases': [
24 {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } 21 {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() }
25 ] 22 ]
26 } 23 }
27 } 24 }
28 25
29 #save info to json file 26 #save info to json file
30 with open( sys.argv[1], 'wb' ) as out: 27 with open( sys.argv[1], 'wb' ) as out: