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

planemo upload for repository https://github.com/galaxyproject/tools-devteam/tree/master/data_managers/data_manager_gemini_downloader commit 2bffef0f9e5d35ae0af1f74f044b5b1431b01d32-dirty

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/data_manager/data_manager_gemini_download.py	Tue Dec 29 10:58:29 2015 -0500
@@ -0,0 +1,32 @@
+#!/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()
+