Mercurial > repos > dfornika > data_manager_build_kraken2_database
view data_manager/kraken2_build_minikraken.py @ 16:d9f190088154 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty
author | dfornika |
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date | Tue, 05 Mar 2019 16:45:43 -0500 |
parents | 9385ea32f9ac |
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#!/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()