Mercurial > repos > iuc > data_manager_gemini_downloader

annotate data_manager/data_manager_gemini_download.py @ 0:7848037cb701 draft default tip

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
author iuc
date Tue, 29 Dec 2015 10:58:29 -0500
parents
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
1 #!/usr/bin/env python
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
2
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
3 import sys
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
4 import os
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
5 import json
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
6 import shlex
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
7 import datetime
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
8 import subprocess
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
9
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
10 def main():
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
11
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
12 today = datetime.date.today()
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
13 params = json.loads( open( sys.argv[1] ).read() )
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
14 target_directory = params[ 'output_data' ][0]['extra_files_path']
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
15 os.mkdir( target_directory )
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
16 cmd = "gemini --annotation-dir %s update --dataonly %s %s" % (target_directory, params['param_dict']['gerp_bp'], params['param_dict']['cadd'] )
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
17 ret = subprocess.check_call( cmd, shell=True )
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
18 data_manager_dict = {
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
19 'data_tables':
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
20 {'gemini_databases': [
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
21 {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() }
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
22 ]
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
23 }
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
24 }
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
25
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
26 #save info to json file
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
27 with open( sys.argv[1], 'wb' ) as out:
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
28 out.write( json.dumps( data_manager_dict ) )
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
29
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
30 if __name__ == "__main__":
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
31 main()
7848037cb701 planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty
iuc
parents:
diff changeset
32