Mercurial > repos > dfornika > data_manager_build_kraken2_database
diff data_manager/kraken2_build_standard.py @ 1:32d04371ed19 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
author | dfornika |
---|---|
date | Thu, 28 Feb 2019 13:59:33 -0500 |
parents | 7e43f66abe9d |
children | 1f6fe9dc5490 |
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--- a/data_manager/kraken2_build_standard.py Thu Feb 28 02:32:38 2019 -0500 +++ b/data_manager/kraken2_build_standard.py Thu Feb 28 13:59:33 2019 -0500 @@ -27,13 +27,22 @@ '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), '--db', database_name ] - pprint(args) proc = subprocess.Popen(args=args, shell=False, cwd=target_directory) return_code = proc.wait() if return_code: print("Error building database.", file=sys.stderr) sys.exit( return_code ) - + args = [ + 'kraken2-build', + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', database_name + ] + proc = subprocess.Popen(args=args, shell=False, cwd=target_directory) + return_code = proc.wait() + if return_code: + print("Error building database.", file=sys.stderr) + sys.exit( return_code ) data_table_entry = { "value": database_name, "name": database_name,