Mercurial > repos > iuc > data_manager_gemini_database_downloader
changeset 7:5bcf0e24f42c draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_gemini_database_downloader commit 73ea765822334d9afc2f7b2ef4ddfc1a3fd4289e"
| author | iuc |
|---|---|
| date | Thu, 14 May 2020 05:08:26 -0400 |
| parents | f57426daa04d |
| children | 52b6a4d98009 |
| files | data_manager/data_manager_gemini_download.py |
| diffstat | 1 files changed, 6 insertions(+), 6 deletions(-) [+] |
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--- a/data_manager/data_manager_gemini_download.py Fri Jan 11 17:33:55 2019 -0500 +++ b/data_manager/data_manager_gemini_download.py Thu May 14 05:08:26 2020 -0400 @@ -16,9 +16,9 @@ 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 ) + params = json.loads(open(sys.argv[1]).read()) + target_directory = params['output_data'][0]['extra_files_path'] + os.mkdir(target_directory) # Generate a minimal configuration file for GEMINI update # to instruct the tool to download the annotation data into a @@ -39,7 +39,7 @@ params['param_dict']['gerp_bp'], params['param_dict']['cadd'] ) - subprocess.check_call( cmd, shell=True, env=gemini_env ) + subprocess.check_call(cmd, shell=True, env=gemini_env) # GEMINI tool wrappers that need access to the annotation files # are supposed to symlink them into a gemini/data subfolder of @@ -83,8 +83,8 @@ } # ... and save it to the json results file - with open( sys.argv[1], 'wb' ) as out: - out.write( json.dumps( data_manager_dict ) ) + with open(sys.argv[1], 'w') as out: + out.write(json.dumps(data_manager_dict)) if __name__ == "__main__":