Mercurial > repos > dfornika > data_manager_build_kraken2_database
changeset 17:4c9f9d6098eb draft
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit db9eb9472b9f6caea6a0755697ee8d3a93e85b5b-dirty
| author | dfornika |
|---|---|
| date | Mon, 06 May 2019 19:42:14 -0400 |
| parents | d9f190088154 |
| children | f005b6efd096 |
| files | data_manager/kraken2_build_custom.py data_manager/kraken2_build_custom.xml data_manager/kraken2_build_database.py data_manager/kraken2_build_database.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 data_manager_conf.xml |
| diffstat | 11 files changed, 417 insertions(+), 673 deletions(-) [+] |
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--- a/data_manager/kraken2_build_custom.py Tue Mar 05 16:45:43 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,126 +0,0 @@ -#!/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 - -from pprint import pprint - -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(data_manager_dict, kraken2_args, database_name, params, target_directory, data_table_name=DATA_TABLE_NAME): - today = datetime.date.today().isoformat() - - args = [ - '--threads', str(kraken2_args["threads"]), - '--download-taxonomy', - '--db', database_name - ] - - run(['kraken2-build'] + args, target_directory) - - args = [ - '--threads', str(kraken2_args["threads"]), - '--add-to-library', kraken2_args["fasta"], - '--db', database_name - ] - - run(['kraken2-build'] + args, 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 - ] - - run(['kraken2-build'] + args, target_directory) - - args = [ - '--threads', str(kraken2_args["threads"]), - '--clean', - '--db', database_name - ] - - run(['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()) - pprint(params) - 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, - params, - target_directory - ) - - # save info to json file - open(args.params, 'wb').write(json.dumps(data_manager_dict)) - - -if __name__ == "__main__": - main()
--- a/data_manager/kraken2_build_custom.xml Tue Mar 05 16:45:43 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,35 +0,0 @@ -<?xml version="1.0"?> -<tool id="kraken2_build_custom" name="Kraken2 Custom Database Builder" tool_type="manage_data" version="2.0.7_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_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>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kraken2_build_database.py Mon May 06 19:42:14 2019 -0400 @@ -0,0 +1,332 @@ +#!/usr/bin/env python + +from __future__ import print_function + +import argparse +import datetime +import errno +import json +import os +import shutil +import subprocess +import sys +import tarfile +from enum import Enum + +try: + # Python3 + from urllib.request import urlopen +except ImportError: + from urllib2 import urlopen + + +DATA_TABLE_NAME = "kraken2_databases" + + +class KrakenDatabaseTypes(Enum): + standard = 'standard' + minikraken = 'minikraken' + special = 'special' + custom = 'custom' + + def __str__(self): + return self.value + + +class SpecialDatabaseTypes(Enum): + rdp = 'rdp' + greengenes = 'greengenes' + silva = 'silva' + + def __str__(self): + return self.value + + +class Minikraken2Versions(Enum): + v1 = 'v1' + v2 = 'v2' + + def __str__(self): + return self.value + + +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 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 kraken2_build_special(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_database_type"], + "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_database_type"]], + "(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_database_type"], + '--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 kraken2_build_custom(data_manager_dict, kraken2_args, custom_database_name, target_directory, data_table_name=DATA_TABLE_NAME): + + args = [ + '--threads', str(kraken2_args["threads"]), + '--download-taxonomy', + '--db', custom_database_name + ] + + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + + args = [ + '--threads', str(kraken2_args["threads"]), + '--add-to-library', kraken2_args["custom_fasta"], + '--db', custom_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', custom_database_name + ] + + subprocess.check_call(['kraken2-build'] + args, cwd=target_directory) + + args = [ + '--threads', str(kraken2_args["threads"]), + '--clean', + '--db', custom_database_name + ] + + subprocess.check_call(['kraken2-build'] + args, target_directory) + + data_table_entry = { + "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 + + +def main(): + parser = argparse.ArgumentParser() + parser.add_argument('data_manager_json') + 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') + parser.add_argument('--threads', dest='threads', default=1, help='threads') + parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build') + 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)' ) + 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 = {} + + print(args.database_type) + if str(args.database_type) == 'standard': + kraken2_args = { + "kmer_len": args.kmer_len, + "minimizer_len": args.minimizer_len, + "minimizer_spaces": args.minimizer_spaces, + "threads": args.threads, + } + kraken2_build_standard( + data_manager_output, + kraken2_args, + target_directory, + ) + elif str(args.database_type) == 'minikraken': + kraken2_build_minikraken( + data_manager_output, + str(args.minikraken2_version), + target_directory + ) + elif str(args.database_type) == 'special': + kraken2_args = { + "special_database_type": str(args.special_database_type), + "kmer_len": args.kmer_len, + "minimizer_len": args.minimizer_len, + "minimizer_spaces": args.minimizer_spaces, + "threads": args.threads, + } + kraken2_build_special( + data_manager_output, + kraken2_args, + target_directory, + ) + elif str(args.database_type) == 'custom': + kraken2_args = { + "custom_fasta": args.custom_fasta, + "kmer_len": args.kmer_len, + "minimizer_len": args.minimizer_len, + "minimizer_spaces": args.minimizer_spaces, + "threads": args.threads, + } + kraken2_build_custom( + data_manager_output, + kraken2_args, + args.custom_database_name, + target_directory, + ) + else: + sys.exit("Invalid database type") + + open(args.data_manager_json, 'w').write(json.dumps(data_manager_output)) + + +if __name__ == "__main__": + main()
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/data_manager/kraken2_build_database.xml Mon May 06 19:42:14 2019 -0400 @@ -0,0 +1,84 @@ +<?xml version="1.0"?> +<tool id="kraken2_build_database" name="Kraken2 Database Builder" tool_type="manage_data" version="2.0.8_beta"> + <macros> + <xml name="common_params"> + <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" /> + </xml> + </macros> + <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_database.py' + '${out_file}' + --database-type ${database_type.database_type} + #if $database_type.database_type == "minikraken" + --minikraken2-version ${database_type.minikraken2_version} + #else if $database_type.database_type == "standard" + --threads \${GALAXY_SLOTS:-1} + --kmer-len ${database_type.kmer_len} + --minimizer-len ${database_type.minimizer_len} + --minimizer-spaces ${database_type.minimizer_spaces} + #else if $database_type.database_type == "special" + --threads \${GALAXY_SLOTS:-1} + --special-database-type ${database_type.special_database_type} + --kmer-len ${database_type.kmer_len} + --minimizer-len ${database_type.minimizer_len} + --minimizer-spaces ${database_type.minimizer_spaces} + #else if $database_type.database_type == "custom" + --threads \${GALAXY_SLOTS:-1} + --custom-fasta ${database_type.custom_fasta} + --custom-database-name ${database_type.custom_database_name} + --kmer-len ${database_type.kmer_len} + --minimizer-len ${database_type.minimizer_len} + --minimizer-spaces ${database_type.minimizer_spaces} + #end if + ]]> + </command> + <inputs> + <conditional name="database_type"> + <param name="database_type" type="select" multiple="false" label="Database Type"> + <option value="standard">Standard</option> + <option value="minikraken">MiniKraken</option> + <option value="special">Special</option> + <option value="custom">Custom</option> + </param> + <when value="standard"> + <expand macro="common_params" /> + </when> + <when value="minikraken"> + <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> + </when> + <when value="special"> + <param name="special_database_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> + <expand macro="common_params" /> + </when> + <when value="custom"> + <param name="custom_fasta" type="data" format="fasta" multiple="False" optional="true" label="Select history item" /> + <param name="custom_database_name" type="text" label="Name for this database" /> + <expand macro="common_params" /> + </when> + + </conditional> + </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>
--- a/data_manager/kraken2_build_minikraken.py Tue Mar 05 16:45:43 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,114 +0,0 @@ -#!/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 = [ - '-p', - database_path, - ] - - run(['mkdir'] + args, target_directory) - - args = [ - '-xvzf', - 'minikraken2_' + minikraken2_version + '_8GB.tgz', - '-C', - database_path, - ] - - 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()
--- a/data_manager/kraken2_build_minikraken.xml Tue Mar 05 16:45:43 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,30 +0,0 @@ -<?xml version="1.0"?> -<tool id="kraken2_build_minikraken" name="Kraken2 MiniKraken2 Database Builder" tool_type="manage_data" version="2.0.7_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="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>
--- a/data_manager/kraken2_build_special.py Tue Mar 05 16:45:43 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,130 +0,0 @@ -#!/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_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 - ] - - run(['kraken2-build'] + args, target_directory) - - args = [ - '--threads', str(kraken2_args["threads"]), - '--clean', - '--db', database_path - ] - - run(['kraken2-build'] + 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( '-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, 'wb').write(json.dumps(data_manager_output)) - - -if __name__ == "__main__": - main()
--- a/data_manager/kraken2_build_special.xml Tue Mar 05 16:45:43 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,37 +0,0 @@ -<?xml version="1.0"?> -<tool id="kraken2_build_special" name="Kraken2 Special Database Builder" tool_type="manage_data" version="2.0.7_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_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>
--- a/data_manager/kraken2_build_standard.py Tue Mar 05 16:45:43 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,121 +0,0 @@ -#!/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_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 - ] - - run(['kraken2-build'] + args, target_directory) - - args = [ - '--threads', str(kraken2_args["threads"]), - '--clean', - '--db', database_path - ] - - run(['kraken2-build'] + 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( '-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, 'wb').write(json.dumps(data_manager_output)) - - -if __name__ == "__main__": - main()
--- a/data_manager/kraken2_build_standard.xml Tue Mar 05 16:45:43 2019 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,31 +0,0 @@ -<?xml version="1.0"?> -<tool id="kraken2_build_standard" name="Kraken2 Standard Database Builder" tool_type="manage_data" version="2.0.7_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}' - --threads \${GALAXY_SLOTS:-1} - --kmer-len ${kmer_len} - --minimizer-len ${minimizer_len} - --minimizer-spaces ${minimizer_spaces} - ]]> - </command> - <inputs> - <param name="kmer_len" type="integer" value="35" label="K-mer length in BP" /> - <param name="minimizer_len" type="integer" value="31" label="Minimizer length" /> - <param name="minimizer_spaces" type="integer" value="6" label="Minimizer spaces" /> - </inputs> - <outputs> - <data name="out_file" format="data_manager_json" /> - </outputs> - <help> - </help> - <citations> - <citation type="doi">10.1186/gb-2014-15-3-r46</citation> - </citations> -</tool>
--- a/data_manager_conf.xml Tue Mar 05 16:45:43 2019 -0500 +++ b/data_manager_conf.xml Mon May 06 19:42:14 2019 -0400 @@ -1,5 +1,5 @@ <data_managers> - <data_manager tool_file="data_manager/kraken2_build_standard.xml" id="kraken2_build_standard" version="1.0"> + <data_manager tool_file="data_manager/kraken2_build_database.xml" id="kraken2_build_database" version="1.0"> <data_table name="kraken2_databases"> <output> <column name="value"/> @@ -15,52 +15,4 @@ </output> </data_table> </data_manager> - <data_manager tool_file="data_manager/kraken2_build_custom.xml" id="kraken2_build_custom" version="1.0"> - <data_table name="kraken2_databases"> - <output> - <column name="value"/> - <column name="name"/> - <column name="path" output_ref="out_file"> - <move type="directory"> - <source>${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_manager tool_file="data_manager/kraken2_build_special.xml" id="kraken2_build_special" 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/${path}</value_translation> - <value_translation type="function">abspath</value_translation> - </column> - </output> - </data_table> - </data_manager> - <data_manager tool_file="data_manager/kraken2_build_minikraken.xml" id="kraken2_build_minikraken" version="1.0"> - <data_table name="kraken2_databases"> - <output> - <column name="value"/> - <column name="name"/> - <column name="path" output_ref="out_file"> - <move type="directory"> - <source>${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>