Mercurial > repos > iuc > data_manager_gemini_database_downloader
comparison 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 |
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date | Tue, 04 Apr 2017 18:09:05 -0400 |
parents | 345412d58d75 |
children | fe5a9a7d95b0 |
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2:345412d58d75 | 3:172815da3d41 |
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1 #!/usr/bin/env python | 1 #!/usr/bin/env python |
2 | 2 |
3 import datetime | |
4 import json | |
5 import os | |
6 import subprocess | |
3 import sys | 7 import sys |
4 import os | 8 |
5 import json | |
6 import shlex | |
7 import datetime | |
8 import subprocess | |
9 | 9 |
10 def main(): | 10 def main(): |
11 | |
12 today = datetime.date.today() | 11 today = datetime.date.today() |
13 params = json.loads( open( sys.argv[1] ).read() ) | 12 params = json.loads( open( sys.argv[1] ).read() ) |
14 target_directory = params[ 'output_data' ][0]['extra_files_path'] | 13 target_directory = params[ 'output_data' ][0]['extra_files_path'] |
15 os.mkdir( target_directory ) | 14 os.mkdir( target_directory ) |
16 cmd = "gemini --annotation-dir %s update --dataonly %s %s" % (target_directory, params['param_dict']['gerp_bp'], params['param_dict']['cadd'] ) | 15 cmd = "gemini --annotation-dir %s update --dataonly %s %s" % (target_directory, params['param_dict']['gerp_bp'], params['param_dict']['cadd'] ) |
17 ret = subprocess.check_call( cmd, shell=True ) | 16 subprocess.check_call( cmd, shell=True ) |
18 data_manager_dict = { | 17 data_manager_dict = { |
19 'data_tables': | 18 'data_tables': { |
20 {'gemini_databases': [ | 19 'gemini_databases': [ |
21 {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } | 20 {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } |
22 ] | 21 ] |
23 } | 22 } |
24 } | 23 } |
25 | 24 |
26 #save info to json file | 25 # save info to json file |
27 with open( sys.argv[1], 'wb' ) as out: | 26 with open( sys.argv[1], 'wb' ) as out: |
28 out.write( json.dumps( data_manager_dict ) ) | 27 out.write( json.dumps( data_manager_dict ) ) |
29 | 28 |
29 | |
30 if __name__ == "__main__": | 30 if __name__ == "__main__": |
31 main() | 31 main() |
32 |