Mercurial > repos > iuc > data_manager_gemini_database_downloader
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
author | iuc |
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date | Thu, 18 Feb 2016 08:49:06 -0500 |
parents | fd9e9ac5ecb3 |
children | 172815da3d41 |
rev | line source |
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0 | 1 #!/usr/bin/env python |
2 | |
3 import sys | |
4 import os | |
5 import json | |
6 import shlex | |
7 import datetime | |
8 import subprocess | |
9 | |
10 def main(): | |
11 | |
12 today = datetime.date.today() | |
13 params = json.loads( open( sys.argv[1] ).read() ) | |
14 target_directory = params[ 'output_data' ][0]['extra_files_path'] | |
15 os.mkdir( target_directory ) | |
2
345412d58d75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_database_downloader commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
0
diff
changeset
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16 cmd = "gemini --annotation-dir %s update --dataonly %s %s" % (target_directory, params['param_dict']['gerp_bp'], params['param_dict']['cadd'] ) |
0 | 17 ret = subprocess.check_call( cmd, shell=True ) |
2
345412d58d75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_database_downloader commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
0
diff
changeset
|
18 data_manager_dict = { |
345412d58d75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_database_downloader commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
0
diff
changeset
|
19 'data_tables': |
345412d58d75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_database_downloader commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
0
diff
changeset
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20 {'gemini_databases': [ |
345412d58d75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_database_downloader commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
0
diff
changeset
|
21 {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } |
345412d58d75
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_database_downloader commit 4bbfca6f0e9cae9a8f263aad4eab7304c96358c4
iuc
parents:
0
diff
changeset
|
22 ] |
0 | 23 } |
24 } | |
25 | |
26 #save info to json file | |
27 with open( sys.argv[1], 'wb' ) as out: | |
28 out.write( json.dumps( data_manager_dict ) ) | |
29 | |
30 if __name__ == "__main__": | |
31 main() | |
32 |