Previous changeset 51:2fd3ebc4fcf3 (2019-05-03) Next changeset 53:21cd25cc1ab2 (2019-05-08) |
Commit message:
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 1137710d16538da15bcd87e1ba382e2afc00031f-dirty |
modified:
data_manager/kraken2_build_database.py data_manager/kraken2_build_database.xml data_manager_conf.xml |
removed:
data_manager/kraken2_build_custom.py data_manager/kraken2_build_custom.xml data_manager/kraken2_build_minikraken.py data_manager/kraken2_build_minikraken.xml data_manager/kraken2_build_special.py data_manager/kraken2_build_special.xml data_manager/kraken2_build_standard.py data_manager/kraken2_build_standard.xml |
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diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_custom.py --- a/data_manager/kraken2_build_custom.py Fri May 03 19:38:34 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,113 +0,0 @@ -#!/usr/bin/env python - -from __future__ import print_function - -import argparse -import errno -import json -import os -import subprocess - - -DATA_TABLE_NAME = "kraken2_databases" - - -def kraken2_build(data_manager_dict, kraken2_args, database_name, target_directory, data_table_name=DATA_TABLE_NAME): - - args = [ - '--threads', str(kraken2_args["threads"]), - '--download-taxonomy', - '--db', database_name - ] - - subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) - - args = [ - '--threads', str(kraken2_args["threads"]), - '--add-to-library', kraken2_args["fasta"], - '--db', database_name - ] - - subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) - - args = [ - '--threads', str(kraken2_args["threads"]), - '--build', - '--kmer-len', str(kraken2_args["kmer_len"]), - '--minimizer-len', str(kraken2_args["minimizer_len"]), - '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), - '--db', database_name - ] - - subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) - - args = [ - '--threads', str(kraken2_args["threads"]), - '--clean', - '--db', database_name - ] - - subprocess.check_call(['kraken2-build'] + args, target_directory) - - 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( '-d', '--db', dest='database_name', help='database name' ) - 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( '-f', '--fasta', dest='fasta', help='fasta' ) - 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, - "fasta": args.fasta, - "threads": args.threads, - } - - 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( - data_manager_dict, - kraken2_args, - args.database_name, - target_directory - ) - - # save info to json file - open(args.params, 'w').write(json.dumps(data_manager_dict)) - - -if __name__ == "__main__": - main() |
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diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_custom.xml --- a/data_manager/kraken2_build_custom.xml Fri May 03 19:38:34 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,35 +0,0 @@ -<?xml version="1.0"?> -<tool id="kraken2_build_custom" name="Kraken2 Custom Database Builder" tool_type="manage_data" version="2.0.8_beta"> - <description>database builder</description> - <requirements> - <requirement type="package" version="2.0.8_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_custom.py' - '${out_file}' - --threads \${GALAXY_SLOTS:-1} - --db '${database_name}' - --kmer-len ${kmer_len} - --minimizer-len ${minimizer_len} - --minimizer-spaces ${minimizer_spaces} - --fasta ${input_fasta} - ]]> - </command> - <inputs> - <param name="input_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" /> - <param name="database_name" type="text" label="Name for this database" /> - <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 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_database.py --- a/data_manager/kraken2_build_database.py Fri May 03 19:38:34 2019 -0400 +++ b/data_manager/kraken2_build_database.py Wed May 08 18:39:03 2019 -0400 |
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@@ -50,7 +50,7 @@ return self.value -def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME): +def kraken2_build_standard(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME): now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") database_value = "_".join([ @@ -92,15 +92,21 @@ subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = { - "value": database_value, - "name": database_name, - "path": database_path, + 'data_tables': { + data_table_name: [ + { + "value": database_value, + "name": database_name, + "path": database_path, + } + ] + } } - _add_data_table_entry(data_manager_dict, data_table_entry) + return data_table_entry -def kraken2_build_minikraken(data_manager_dict, minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME): +def kraken2_build_minikraken(minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME): now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") @@ -130,15 +136,21 @@ fh.extractall(target_directory) data_table_entry = { - "value": database_value, - "name": database_name, - "path": database_value, + 'data_tables': { + data_table_name: [ + { + "value": database_value, + "name": database_name, + "path": database_value, + } + ] + } } - _add_data_table_entry(data_manager_dict, data_table_entry) + return data_table_entry -def kraken2_build_special(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME): +def kraken2_build_special(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME): now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") @@ -187,15 +199,21 @@ subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) data_table_entry = { - "value": database_value, - "name": database_name, - "path": database_path, + 'data_tables': { + data_table_name: [ + { + "value": database_value, + "name": database_name, + "path": database_path, + } + ] + } } - _add_data_table_entry(data_manager_dict, data_table_entry) + return data_table_entry -def kraken2_build_custom(data_manager_dict, kraken2_args, custom_database_name, target_directory, data_table_name=DATA_TABLE_NAME): +def kraken2_build_custom(kraken2_args, custom_database_name, target_directory, data_table_name=DATA_TABLE_NAME): args = [ '--threads', str(kraken2_args["threads"]), @@ -233,24 +251,23 @@ subprocess.check_call(['kraken2-build'] + args, target_directory) data_table_entry = { - "value": custom_database_name, - "name": custom_database_name, - "path": custom_database_name + 'data_tables': { + data_table_name: [ + { + "value": custom_database_name, + "name": custom_database_name, + "path": custom_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_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 + return data_table_entry def main(): parser = argparse.ArgumentParser() - parser.add_argument('data_manager_json') + parser.add_argument('--extra-files-path', dest='extra_files_path', help='') parser.add_argument('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length') parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length') parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces') @@ -259,12 +276,12 @@ parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)') parser.add_argument('--special-database-type', dest='special_database_type', type=SpecialDatabaseTypes, choices=list(SpecialDatabaseTypes), help='type of special database to build (only applies to --database-type special)') parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)') - parser.add_argument( '--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)' ) + parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)') 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'] + target_directory = args.extra_files_path try: os.mkdir( target_directory ) @@ -276,7 +293,6 @@ data_manager_output = {} - print(args.database_type) if str(args.database_type) == 'standard': kraken2_args = { "kmer_len": args.kmer_len, @@ -284,14 +300,12 @@ "minimizer_spaces": args.minimizer_spaces, "threads": args.threads, } - kraken2_build_standard( - data_manager_output, + data_manager_output = kraken2_build_standard( kraken2_args, target_directory, ) elif str(args.database_type) == 'minikraken': - kraken2_build_minikraken( - data_manager_output, + data_manager_output = kraken2_build_minikraken( str(args.minikraken2_version), target_directory ) @@ -303,8 +317,7 @@ "minimizer_spaces": args.minimizer_spaces, "threads": args.threads, } - kraken2_build_special( - data_manager_output, + data_manager_output = kraken2_build_special( kraken2_args, target_directory, ) @@ -316,8 +329,7 @@ "minimizer_spaces": args.minimizer_spaces, "threads": args.threads, } - kraken2_build_custom( - data_manager_output, + data_manager_output = kraken2_build_custom( kraken2_args, args.custom_database_name, target_directory, |
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diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_database.xml --- a/data_manager/kraken2_build_database.xml Fri May 03 19:38:34 2019 -0400 +++ b/data_manager/kraken2_build_database.xml Wed May 08 18:39:03 2019 -0400 |
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@@ -15,7 +15,7 @@ <command detect_errors="exit_code"> <![CDATA[ python '$__tool_directory__/kraken2_build_database.py' - '${out_file}' + --extra-files-path '$out_file.extra_files_path' --database-type ${database_type.database_type} #if $database_type.database_type == "minikraken" --minikraken2-version ${database_type.minikraken2_version} |
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diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_minikraken.py --- a/data_manager/kraken2_build_minikraken.py Fri May 03 19:38:34 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,100 +0,0 @@ -#!/usr/bin/env python - -from __future__ import print_function - -import argparse -import datetime -import errno -import json -import os -import shutil -import tarfile - -try: - # Python3 - from urllib.request import urlopen -except ImportError: - from urllib2 import urlopen - - -DATA_TABLE_NAME = "kraken2_databases" - - -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 + ")" - ]) - - # download the minikraken2 data - src = urlopen( - 'ftp://ftp.ccb.jhu.edu/pub/data/kraken2_dbs/minikraken2_%s_8GB_201904_UPDATE.tgz' - % minikraken2_version - ) - with open('tmp_data.tar.gz', 'wb') as dst: - shutil.copyfileobj(src, dst) - # unpack the downloaded archive to the target directory - with tarfile.open('tmp_data.tar.gz', 'r:gz') as fh: - fh.extractall(target_directory) - - data_table_entry = { - "value": database_value, - "name": database_name, - "path": database_value, - } - - _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, 'w').write(json.dumps(data_manager_output)) - - -if __name__ == "__main__": - main() |
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diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_minikraken.xml --- a/data_manager/kraken2_build_minikraken.xml Fri May 03 19:38:34 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,30 +0,0 @@ -<?xml version="1.0"?> -<tool id="kraken2_build_minikraken" name="Kraken2 MiniKraken2 Database Builder" tool_type="manage_data" version="2.0.8_beta"> - <description>database builder</description> - <requirements> - <requirement type="package" version="2.0.8_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="v2">Version 2</option> - <option value="v1">Version 1</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 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_special.py --- a/data_manager/kraken2_build_special.py Fri May 03 19:38:34 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,122 +0,0 @@ -#!/usr/bin/env python - -from __future__ import print_function - -import argparse -import datetime -import errno -import json -import os -import subprocess - - -DATA_TABLE_NAME = "kraken2_databases" - - -def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME): - - now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ") - - special_database_names = { - "rdp": "RDP", - "greengenes": "Greengenes", - "silva": "Silva", - } - - database_value = "_".join([ - now, - kraken2_args["special"], - "kmer-len", str(kraken2_args["kmer_len"]), - "minimizer-len", str(kraken2_args["minimizer_len"]), - "minimizer-spaces", str(kraken2_args["minimizer_spaces"]), - ]) - - database_name = " ".join([ - special_database_names[kraken2_args["special"]], - "(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"]), - '--special', kraken2_args["special"], - '--kmer-len', str(kraken2_args["kmer_len"]), - '--minimizer-len', str(kraken2_args["minimizer_len"]), - '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), - '--db', database_path - ] - - subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) - - args = [ - '--threads', str(kraken2_args["threads"]), - '--clean', - '--db', database_path - ] - - subprocess.check_call(['kraken2-build'] + args, cwd=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( '-b', '--db-type', dest='db_type', help='database type (one of: silva, rdp, greengenes)' ) - 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 = { - "special": args.db_type, - "kmer_len": args.kmer_len, - "minimizer_len": args.minimizer_len, - "minimizer_spaces": args.minimizer_spaces, - "threads": args.threads, - } - - 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_standard( - data_manager_output, - kraken2_args, - target_directory, - ) - - open(args.data_manager_json, 'w').write(json.dumps(data_manager_output)) - - -if __name__ == "__main__": - main() |
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diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_special.xml --- a/data_manager/kraken2_build_special.xml Fri May 03 19:38:34 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,37 +0,0 @@ -<?xml version="1.0"?> -<tool id="kraken2_build_special" name="Kraken2 Special Database Builder" tool_type="manage_data" version="2.0.8_beta"> - <description>database builder</description> - <requirements> - <requirement type="package" version="2.0.8_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_special.py' - '${out_file}' - --db-type ${db_type} - --threads \${GALAXY_SLOTS:-1} - --kmer-len ${kmer_len} - --minimizer-len ${minimizer_len} - --minimizer-spaces ${minimizer_spaces} - ]]> - </command> - <inputs> - <param name="db_type" type="select" multiple="false" label="Select database to build"> - <option value="greengenes">Greengenes</option> - <option value="silva">Silva</option> - <option value="rdp">RDP</option> - </param> - <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 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_standard.py --- a/data_manager/kraken2_build_standard.py Fri May 03 19:38:34 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,113 +0,0 @@ -#!/usr/bin/env python - -from __future__ import print_function - -import argparse -import datetime -import errno -import json -import os -import subprocess - - -DATA_TABLE_NAME = "kraken2_databases" - - -def kraken2_build_standard(data_manager_dict, kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME): - 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"]), - ]) - - 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_path - ] - - subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) - - args = [ - '--threads', str(kraken2_args["threads"]), - '--clean', - '--db', database_path - ] - - subprocess.check_call(['kraken2-build'] + args, cwd=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( '-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, - } - - 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_standard( - data_manager_output, - kraken2_args, - target_directory, - ) - - open(args.data_manager_json, 'w').write(json.dumps(data_manager_output)) - - -if __name__ == "__main__": - main() |
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diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager/kraken2_build_standard.xml --- a/data_manager/kraken2_build_standard.xml Fri May 03 19:38:34 2019 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 |
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@@ -1,31 +0,0 @@ -<?xml version="1.0"?> -<tool id="kraken2_build_standard" name="Kraken2 Standard Database Builder" tool_type="manage_data" version="2.0.8_beta"> - <description>database builder</description> - <requirements> - <requirement type="package" version="2.0.8_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}' - --threads \${GALAXY_SLOTS:-1} - --kmer-len ${kmer_len} - --minimizer-len ${minimizer_len} - --minimizer-spaces ${minimizer_spaces} - ]]> - </command> - <inputs> - <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> - <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> - <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> - </inputs> - <outputs> - <data name="out_file" format="data_manager_json" /> - </outputs> - <help> - </help> - <citations> - <citation type="doi">10.1186/gb-2014-15-3-r46</citation> - </citations> -</tool> |
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diff -r 2fd3ebc4fcf3 -r 86bc169b0aeb data_manager_conf.xml --- a/data_manager_conf.xml Fri May 03 19:38:34 2019 -0400 +++ b/data_manager_conf.xml Wed May 08 18:39:03 2019 -0400 |
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@@ -1,18 +1,18 @@ <data_managers> <data_manager tool_file="data_manager/kraken2_build_database.xml" id="kraken2_build_database" version="1.0"> - <data_table name="kraken2_databases"> - <output> - <column name="value"/> - <column name="name"/> - <column name="path" output_ref="out_file"> - <move type="directory"> - <source>${path}</source> - <target base="${GALAXY_DATA_MANAGER_DATA_PATH}">kraken2_databases/${path}</target> - </move> + <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> + <value_translation type="function">abspath</value_translation> + </column> + </output> + </data_table> </data_manager> </data_managers> |