Mercurial > repos > iuc > data_manager_gemini_database_downloader
comparison 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 |
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1:a580422f6f1d | 2:345412d58d75 |
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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: |