comparison 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

0:7e43f66abe9d

        '--kmer-len', str(kraken2_args["kmer_len"]),
        '--minimizer-len', str(kraken2_args["minimizer_len"]),
        '--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 )

    data_table_entry = {
        "value": database_name,
        "name": database_name,
        "path": database_name
    }

1:32d04371ed19

        '--kmer-len', str(kraken2_args["kmer_len"]),
        '--minimizer-len', str(kraken2_args["minimizer_len"]),
        '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
        '--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 )
    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,
        "path": database_name
    }