| Previous changeset 13:48c013603913 (2019-02-28) Next changeset 15:c6db7ff0b3f8 (2019-02-28) |
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Commit message:
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 682a16af9bce01ff23176dbce291034d67947e58-dirty |
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modified:
data_manager/kraken2_build_standard.py data_manager/kraken2_build_standard.xml |
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| diff -r 48c013603913 -r 25298e35048f data_manager/kraken2_build_standard.py --- a/data_manager/kraken2_build_standard.py Thu Feb 28 01:38:45 2019 -0500 +++ b/data_manager/kraken2_build_standard.py Thu Feb 28 01:50:00 2019 -0500 |
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| @@ -15,18 +15,19 @@ DATA_TABLE_NAME = "kraken2_databases" -def kraken2_build_standard(data_manager_dict, kmer_len, minimizer_len, minimizer_spaces, params, target_directory, data_table_name=DATA_TABLE_NAME): +def kraken2_build_standard(data_manager_dict, kraken2_args, params, target_directory, data_table_name=DATA_TABLE_NAME): today = datetime.date.today().isoformat() database_name = "_".join([today, "standard"]) args = [ 'kraken2-build', - '--threads', "${GALAXY_SLOTS:-1}", + '--threads', str(kraken2_args["threads"]), '--standard', - '--kmer-len', str(kmer_len), - '--minimizer-len', str(minimizer_len), - '--minimizer-spaces', str(minimizer_spaces), + '--kmer-len', str(kraken2_args["kmer_len"]), + '--minimizer-len', str(kraken2_args["minimizer_len"]), + '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), '--db', database_name ] + pprint(args) proc = subprocess.Popen(args=args, shell=False, cwd=target_directory) return_code = proc.wait() if return_code: @@ -55,8 +56,16 @@ parser.add_argument( '-k', '--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length' ) parser.add_argument( '-m', '--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length' ) parser.add_argument( '-s', '--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces' ) + parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' ) args = parser.parse_args() + kraken2_args = { + "kmer_len": args.kmer_len, + "minimizer_len": args.minimizer_len, + "minimizer_spaces": args.minimizer_spaces, + "threads": args.threads, + } + params = json.loads(open(args.params).read()) pprint(params) target_directory = params['output_data'][0]['extra_files_path'] @@ -74,9 +83,7 @@ # build the index kraken2_build_standard( data_manager_dict, - args.kmer_len, - args.minimizer_len, - args.minimizer_spaces, + kraken2_args, params, target_directory ) |
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| diff -r 48c013603913 -r 25298e35048f data_manager/kraken2_build_standard.xml --- a/data_manager/kraken2_build_standard.xml Thu Feb 28 01:38:45 2019 -0500 +++ b/data_manager/kraken2_build_standard.xml Thu Feb 28 01:50:00 2019 -0500 |
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| @@ -8,7 +8,8 @@ <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/kraken2_build_standard.py' - '${out_file}' + '${out_file}' + --threads \${GALAXY_SLOTS:-1} --kmer-len ${kmer_len} --minimizer-len ${minimizer_len} --minimizer-spaces ${minimizer_spaces} |