| Previous changeset 7:1088e1592527 (2019-02-27) Next changeset 9:61c1109599f1 (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_standard_database_builder.xml data_manager/make_json.py |
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added:
data_manager/kraken2_build_standard.py data_manager/kraken2_build_standard.xml |
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| diff -r 1088e1592527 -r 85447ce51182 data_manager/kraken2_build_standard.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kraken2_build_standard.py Thu Feb 28 00:37:31 2019 -0500 |
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| @@ -0,0 +1,88 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import argparse +import datetime +import errno +import os +import string +import subprocess +import sys + +from json import dumps, loads + + +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): + today = datetime.date.today().isoformat() + database_name = "_".join(today, "standard") + args = [ + 'kraken2-build', + '--threads', "${GALAXY_SLOTS:-1}", + '--standard', + '--kmer-len', kmer_len, + '--minimizer-len', minimizer_len, + '--minimizer-spaces', 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 ) + + data_table_entry = { + "value": database_name, + "name": database_name, + "path": database_name + } + + _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry) + + +def _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry): + data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} ) + data_manager_dict['data_tables'][ data_table_name ] = data_manager_dict['data_tables'].get( data_table_name, [] ) + data_manager_dict['data_tables'][ data_table_name ].append( data_table_entry ) + return data_manager_dict + + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument('params') + 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' ) + args = parser.parse_args() + + params = json.loads(open(args.params).read()) + target_directory = params['output_data'][0]['extra_files_path'] + + try: + os.mkdir( target_directory ) + except OSError as exc: + if exc.errno == errno.EEXIST and os.path.isdir( target_directory ): + pass + else: + raise + + data_manager_dict = {} + + # build the index + kraken2_build_standard( + data_manager_dict, + args.kmer_len, + args.minimizer_len, + args.minimizer_spaces, + params, + target_directory + ) + + # save info to json file + open(args.params, 'wb').write(json.dumps(data_manager_dict)) + + +if __name__ == "__main__": + main() |
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| diff -r 1088e1592527 -r 85447ce51182 data_manager/kraken2_build_standard.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kraken2_build_standard.xml Thu Feb 28 00:37:31 2019 -0500 |
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| @@ -0,0 +1,30 @@ +<?xml version="1.0"?> +<tool id="kraken2_standard_database_builder__" name="Kraken2 Standard Database Builder" tool_type="manage_data" version="2.0.7_beta"> + <description>database builder</description> + <requirements> + <requirement type="package" version="2.0.7_beta">kraken2</requirement> + </requirements> + <version_command>kraken2 -version | head -n 1 | awk '{print $NF}'</version_command> + <command detect_errors="exit_code"> + <![CDATA[ + python '$__tool_directory__/kraken2_build_standard.py' + '${out_file}' + --kmer-len ${kmer_len} + --minimizer-len ${minimizer_len} + --minimizer-spaces ${minimizer_spaces} + ]]> + </command> + <inputs> + <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> + <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> + <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> + </inputs> + <outputs> + <data name="out_file" format="data_manager_json" /> + </outputs> + <help> + </help> + <citations> + <citation type="doi">10.1186/gb-2014-15-3-r46</citation> + </citations> +</tool> |
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| diff -r 1088e1592527 -r 85447ce51182 data_manager/kraken2_standard_database_builder.xml --- a/data_manager/kraken2_standard_database_builder.xml Wed Feb 27 22:00:10 2019 -0500 +++ b/data_manager/kraken2_standard_database_builder.xml Thu Feb 28 00:37:31 2019 -0500 |
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| @@ -9,7 +9,7 @@ <![CDATA[ #import datetime #set kraken2_db_name = datetime.date.today().strftime('%Y-%m-%d') + "_standard" - mkdir kraken2_database && cd kraken2_database && + mkdir kraken2-database && cd kraken2-database && kraken2-build --standard --threads \${GALAXY_SLOTS:-1} |
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| diff -r 1088e1592527 -r 85447ce51182 data_manager/make_json.py --- a/data_manager/make_json.py Wed Feb 27 22:00:10 2019 -0500 +++ b/data_manager/make_json.py Thu Feb 28 00:37:31 2019 -0500 |
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| @@ -9,11 +9,11 @@ data_manager_entry['value'] = args.database.lower() data_manager_entry['name'] = args.database data_manager_entry['path'] = '.' - data_manager_json = dict(data_tables=dict(kraken_databases=data_manager_entry)) + data_manager_json = dict(data_tables=dict(kraken2_databases=data_manager_entry)) params = json.loads(open(args.output).read()) target_directory = params['output_data'][0]['extra_files_path'] os.mkdir(target_directory) - output_path = os.path.join(os.getcwd(), 'kraken-database') + output_path = os.path.join(os.getcwd(), 'kraken2-database') for filename in os.listdir(output_path): shutil.move(os.path.join(output_path, filename), target_directory) file(args.output, 'w').write(json.dumps(data_manager_json)) |