Mercurial > repos > iuc > data_manager_funannotate

comparison data_manager/funannotate.py @ 2:13018941c6a0 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_funannotate commit 2c9bec50907576e22b02b8ea570073018c635475"
author iuc
date Fri, 19 Nov 2021 11:15:54 +0000
parents 8dff71edbce5
children
comparison
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1:8dff71edbce5 2:13018941c6a0
222 222
223 if __name__ == "__main__": 223 if __name__ == "__main__":
224 224
225 parser = argparse.ArgumentParser() 225 parser = argparse.ArgumentParser()
226 parser.add_argument('--partial', dest='partial', action='store_true', help='Only download a small subset of data (for testing)') 226 parser.add_argument('--partial', dest='partial', action='store_true', help='Only download a small subset of data (for testing)')
227 parser.add_argument('--wget', dest='wget', action='store_true', help='Download using wget (instead of urllib)')
227 parser.add_argument("version_id") 228 parser.add_argument("version_id")
228 parser.add_argument("datatable_name") 229 parser.add_argument("datatable_name")
229 parser.add_argument("galaxy_datamanager_filename") 230 parser.add_argument("galaxy_datamanager_filename")
230 args = parser.parse_args() 231 args = parser.parse_args()
231 232
241 242
242 os.mkdir(output_directory) 243 os.mkdir(output_directory)
243 cmd_args = ['funannotate', 'setup', '-d', output_directory, '-b', 'all'] 244 cmd_args = ['funannotate', 'setup', '-d', output_directory, '-b', 'all']
244 if args.partial: 245 if args.partial:
245 cmd_args += ['-i', 'merops', '-b', 'eukaryota'] 246 cmd_args += ['-i', 'merops', '-b', 'eukaryota']
247 if args.wget:
248 cmd_args += ['--wget']
246 proc = subprocess.Popen(args=cmd_args, shell=False, cwd=output_directory) 249 proc = subprocess.Popen(args=cmd_args, shell=False, cwd=output_directory)
247 return_code = proc.wait() 250 return_code = proc.wait()
248 if return_code: 251 if return_code:
249 print("Error downloading Funannotate database.", file=sys.stderr) 252 print("Error downloading Funannotate database.", file=sys.stderr)
250 sys.exit(return_code) 253 sys.exit(return_code)