Mercurial > repos > iuc > data_manager_gemini_database_downloader
diff 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 |
|---|---|
| date | Thu, 18 Feb 2016 08:49:06 -0500 |
| parents | fd9e9ac5ecb3 |
| children | 172815da3d41 |
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--- a/data_manager/data_manager_gemini_download.py Tue Aug 26 19:58:38 2014 -0400 +++ b/data_manager/data_manager_gemini_download.py Thu Feb 18 08:49:06 2016 -0500 @@ -10,19 +10,16 @@ def main(): today = datetime.date.today() - gemini_root_dir = os.environ['GEMINI_ROOT_DIR'] params = json.loads( open( sys.argv[1] ).read() ) target_directory = params[ 'output_data' ][0]['extra_files_path'] os.mkdir( target_directory ) - gemini_exec = os.path.join( gemini_root_dir, 'gemini', 'gemini', 'install-data.py' ) - cmd = gemini_exec + " %s %s" % (' '.join( [params['param_dict']['gerp_bp'], params['param_dict']['cadd']] ), target_directory) - #cmd = gemini_exec + " --help > %s/foo.txt" % 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() } - ] + data_manager_dict = { + 'data_tables': + {'gemini_databases': [ + {'value': today.isoformat(), 'dbkey': 'hg19', 'name': 'GEMINI annotations (%s)' % today.isoformat(), 'path': './%s' % today.isoformat() } + ] } }