| Previous changeset 23:0c4e821c704b (2019-03-05) Next changeset 25:370d5fee9c76 (2019-03-05) |
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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 70494d589aa1990618ebc7a895e91477d41c3203-dirty |
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modified:
data_manager/kraken2_build_special.py data_manager/kraken2_build_standard.py data_manager_conf.xml |
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added:
data_manager/kraken2_build_minikraken.py data_manager/kraken2_build_minikraken.xml |
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| diff -r 0c4e821c704b -r 7233538ef3cb data_manager/kraken2_build_minikraken.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kraken2_build_minikraken.py Tue Mar 05 15:10:42 2019 -0500 |
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| @@ -0,0 +1,104 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import argparse +import datetime +import errno +import json +import os +import string +import subprocess +import sys + + +DATA_TABLE_NAME = "kraken2_databases" + +def run(args, cwd): + proc = subprocess.Popen(args=args, shell=False, cwd=cwd) + return_code = proc.wait() + if return_code: + print("Error building database.", file=sys.stderr) + sys.exit( return_code ) + +def kraken2_build_minikraken(data_manager_dict, minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME): + + now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") + + database_value = "_".join([ + now, + "minikraken2", + minikraken2_version, + "8GB", + ]) + + database_name = " ".join([ + "Minikraken2", + minikraken2_version, + "(Created:", + now + ")" + ]) + + database_path = database_value + + args = [ + 'https://ccb.jhu.edu/software/kraken2/dl/minikraken2_' + minikraken2_version + '_8GB.tgz' + ] + + run(['wget'] + args, target_directory) + + args = [ + '-xvzf', 'minikraken2_' + minikraken2_version + '_8GB.tgz' + ] + + run(['tar'] + args, target_directory) + + data_table_entry = { + "value": database_value, + "name": database_name, + "path": database_path, + } + + _add_data_table_entry(data_manager_dict, data_table_entry) + + +def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name=DATA_TABLE_NAME): + 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('data_manager_json') + parser.add_argument( '-v', '--minikraken2-version', dest='minikraken2_version', default="v2", help='MiniKraken2 version (v1 or v2)' ) + parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' ) + + args = parser.parse_args() + + data_manager_input = json.loads(open(args.data_manager_json).read()) + + target_directory = data_manager_input['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_output = {} + + kraken2_build_minikraken( + data_manager_output, + args.minikraken2_version, + target_directory, + ) + + open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output)) + + +if __name__ == "__main__": + main() |
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| diff -r 0c4e821c704b -r 7233538ef3cb data_manager/kraken2_build_minikraken.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kraken2_build_minikraken.xml Tue Mar 05 15:10:42 2019 -0500 |
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| @@ -0,0 +1,30 @@ +<?xml version="1.0"?> +<tool id="kraken2_build_minikraken" name="Kraken2 MiniKraken2 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_minikraken.py' + '${out_file}' + --threads \${GALAXY_SLOTS:-1} + --minikraken2-version ${minikraken2_version} + ]]> + </command> + <inputs> + <param name="minikraken2_version" type="select" multiple="false" label="Select MiniKraken2 database version to download"> + <option value="v1">Version 1</option> + <option value="v2">Version 2</option> + </param> + </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 0c4e821c704b -r 7233538ef3cb data_manager/kraken2_build_special.py --- a/data_manager/kraken2_build_special.py Tue Mar 05 13:11:02 2019 -0500 +++ b/data_manager/kraken2_build_special.py Tue Mar 05 15:10:42 2019 -0500 |
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| @@ -42,7 +42,7 @@ database_name = " ".join([ special_database_names[kraken2_args["special"]], "(Created:", - now + "," + now + ",", "kmer-len=" + str(kraken2_args["kmer_len"]) + ",", "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",", "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")", |
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| diff -r 0c4e821c704b -r 7233538ef3cb data_manager/kraken2_build_standard.py --- a/data_manager/kraken2_build_standard.py Tue Mar 05 13:11:02 2019 -0500 +++ b/data_manager/kraken2_build_standard.py Tue Mar 05 15:10:42 2019 -0500 |
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| @@ -22,21 +22,34 @@ sys.exit( return_code ) def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME): - today = datetime.date.today().isoformat() - database_name = "_".join([ - today, + now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") + + database_value = "_".join([ + now, "standard", - "kmer-len=" + str(kraken2_args["kmer_len"]), - "minimizer-len=" + str(kraken2_args["minimizer_len"]), - "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]), + "kmer-len" + str(kraken2_args["kmer_len"]), + "minimizer-len" + str(kraken2_args["minimizer_len"]), + "minimizer-spaces" + str(kraken2_args["minimizer_spaces"]), ]) + + database_name = " ".join([ + "Standard", + "(Created:", + now + ",", + "kmer-len=" + str(kraken2_args["kmer_len"]) + ",", + "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",", + "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")", + ]) + + database_path = database_value + args = [ '--threads', str(kraken2_args["threads"]), '--standard', '--kmer-len', str(kraken2_args["kmer_len"]), '--minimizer-len', str(kraken2_args["minimizer_len"]), '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), - '--db', database_name + '--db', database_path ] run(['kraken2-build'] + args, target_directory) @@ -44,15 +57,15 @@ args = [ '--threads', str(kraken2_args["threads"]), '--clean', - '--db', database_name + '--db', database_path ] run(['kraken2-build'] + args, target_directory) data_table_entry = { - "value": database_name, + "value": database_value, "name": database_name, - "path": database_name + "path": database_path, } _add_data_table_entry(data_manager_dict, data_table_entry) |
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| diff -r 0c4e821c704b -r 7233538ef3cb data_manager_conf.xml --- a/data_manager_conf.xml Tue Mar 05 13:11:02 2019 -0500 +++ b/data_manager_conf.xml Tue Mar 05 15:10:42 2019 -0500 |
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| @@ -47,4 +47,20 @@ </output> </data_table> </data_manager> + <data_manager tool_file="data_manager/kraken2_build_minikraken.xml" id="kraken2_build_minikraken" version="1.0"> + <data_table name="kraken2_databases"> + <output> + <column name="value"/> + <column name="name"/> + <column name="path" output_ref="out_file"> + <move type="directory"> + <source>${path}</source> + <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases/${path}</target> + </move> + <value_translation>${GALAXY_DATA_MANAGER_DATA_PATH}/kraken2_databases/${path}</value_translation> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> + </data_manager> </data_managers> |