data_manager_build_kraken2_database: data_manager/kraken2_build

annotate data_manager/kraken2_build_database.py @ 5:2f27f3b86827 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"

author	iuc
date	Mon, 08 Nov 2021 15:40:34 +0000
parents	0eebe086fd58
children	9002633b4737

rev	line source
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	1 #!/usr/bin/env python
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	2
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	3 from __future__ import print_function
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	4
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	5 import argparse
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	6 import datetime
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	7 import errno
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	8 import json
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	9 import os
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	10 import shutil
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	11 import subprocess
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	12 import sys
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	13 import tarfile
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	14 from enum import Enum
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	15
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	16 try:
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	17 # Python3
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	18 from urllib.request import urlopen
5 2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	19 from urllib.error import URLError
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	20 except ImportError:
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	21 from urllib2 import urlopen
5 2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	22 from urllib2 import URLError
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	23
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	24
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	25 DATA_TABLE_NAME = "kraken2_databases"
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	26
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	27
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	28 class KrakenDatabaseTypes(Enum):
5 2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	29 standard_local_build = 'standard_local_build'
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	30 standard_prebuilt = 'standard_prebuilt'
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	31 minikraken = 'minikraken'
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	32 special = 'special'
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	33 custom = 'custom'
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	34
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	35 def __str__(self):
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	36 return self.value
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	37
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	38
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	39 class SpecialDatabaseTypes(Enum):
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	40 rdp = 'rdp'
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	41 greengenes = 'greengenes'
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	42 silva = 'silva'
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	43
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	44 def __str__(self):
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	45 return self.value
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	46
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	47
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	48 class Minikraken2Versions(Enum):
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	49 v1 = 'v1'
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	50 v2 = 'v2'
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	51
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	52 def __str__(self):
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	53 return self.value
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	54
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	55
5 2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	56 class StandardPrebuiltSizes(Enum):
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	57 full = 'full'
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	58 gb_16 = '16'
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	59 gb_8 = '8'
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	60
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	61 def __str__(self):
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	62 return self.value
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	63
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	64
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	65 def kraken2_build_standard(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	66 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	67
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	68 database_value = "_".join([
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	69 now,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	70 "standard",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	71 "kmer-len", str(kraken2_args["kmer_len"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	72 "minimizer-len", str(kraken2_args["minimizer_len"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	73 "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
4 0eebe086fd58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e" iuc parents: 3 diff changeset	74 "load-factor", str(kraken2_args["load_factor"]),
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	75 ])
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	76
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	77 database_name = " ".join([
5 2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	78 "Standard (Local Build)",
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	79 "(Created:",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	80 now + ",",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	81 "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	82 "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	83 "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
4 0eebe086fd58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e" iuc parents: 3 diff changeset	84 "load-factor", str(kraken2_args["load_factor"]),
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	85 ])
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	86
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	87 database_path = database_value
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	88
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	89 args = [
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	90 '--threads', str(kraken2_args["threads"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	91 '--standard',
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	92 '--kmer-len', str(kraken2_args["kmer_len"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	93 '--minimizer-len', str(kraken2_args["minimizer_len"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	94 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
4 0eebe086fd58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e" iuc parents: 3 diff changeset	95 '--load-factor', str(kraken2_args["load_factor"]),
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	96 '--db', database_path
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	97 ]
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	98
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	99 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	100
1 6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	101 if kraken2_args["clean"]:
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	102 args = [
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	103 '--threads', str(kraken2_args["threads"]),
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	104 '--clean',
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	105 '--db', database_path
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	106 ]
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	107
1 6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	108 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	109
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	110 data_table_entry = {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	111 'data_tables': {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	112 data_table_name: [
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	113 {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	114 "value": database_value,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	115 "name": database_name,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	116 "path": database_path,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	117 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	118 ]
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	119 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	120 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	121
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	122 return data_table_entry
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	123
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	124
5 2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	125 def kraken2_build_standard_prebuilt(standard_prebuilt_size, prebuilt_date, target_directory, data_table_name=DATA_TABLE_NAME):
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	126
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	127 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	128
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	129 database_value = "_".join([
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	130 now,
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	131 "standard_prebuilt",
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	132 standard_prebuilt_size
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	133 ])
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	134
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	135 database_name = " ".join([
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	136 "Standard (Prebuilt)",
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	137 standard_prebuilt_size,
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	138 "(Downloaded:",
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	139 now + ")"
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	140 ])
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	141
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	142 database_path = database_value
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	143
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	144 size_to_url_str = {
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	145 'full': '',
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	146 '16': '_16gb',
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	147 '8': '_8gb',
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	148 }
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	149 # we may need to let the user choose the date when new DBs are posted.
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	150 date_url_str = prebuilt_date.replace('-', '')
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	151 standard_prebuilt_size_url = size_to_url_str[standard_prebuilt_size]
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	152 # download the pre-built database
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	153 try:
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	154 download_url = 'https://genome-idx.s3.amazonaws.com/kraken/k2_standard%s_%s.tar.gz' % (standard_prebuilt_size_url, date_url_str)
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	155 src = urlopen(download_url)
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	156 except URLError as e:
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	157 print('url: ' + download_url, file=sys.stderr)
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	158 print(e, file=sys.stderr)
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	159 exit(1)
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	160
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	161 with open('tmp_data.tar.gz', 'wb') as dst:
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	162 shutil.copyfileobj(src, dst)
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	163 # unpack the downloaded archive to the target directory
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	164 with tarfile.open('tmp_data.tar.gz', 'r:gz') as fh:
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	165 for member in fh.getmembers():
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	166 if member.isreg():
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	167 member.name = os.path.basename(member.name)
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	168 fh.extract(member, os.path.join(target_directory, database_path))
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	169
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	170 data_table_entry = {
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	171 'data_tables': {
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	172 data_table_name: [
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	173 {
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	174 "value": database_value,
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	175 "name": database_name,
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	176 "path": database_path,
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	177 }
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	178 ]
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	179 }
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	180 }
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	181
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	182 return data_table_entry
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	183
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	184
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	185 def kraken2_build_minikraken(minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME):
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	186
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	187 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	188
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	189 database_value = "_".join([
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	190 now,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	191 "minikraken2",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	192 minikraken2_version,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	193 "8GB",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	194 ])
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	195
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	196 database_name = " ".join([
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	197 "Minikraken2",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	198 minikraken2_version,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	199 "(Created:",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	200 now + ")"
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	201 ])
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	202
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	203 database_path = database_value
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	204
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	205 # download the minikraken2 data
5 2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	206 try:
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	207 download_url = 'https://genome-idx.s3.amazonaws.com/kraken/minikraken2_%s_8GB_201904.tgz' % minikraken2_version
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	208 src = urlopen(download_url)
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	209 except URLError as e:
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	210 print('url: ' + download_url, file=sys.stderr)
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	211 print(e, file=sys.stderr)
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	212 exit(1)
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	213
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	214 with open('tmp_data.tar.gz', 'wb') as dst:
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	215 shutil.copyfileobj(src, dst)
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	216 # unpack the downloaded archive to the target directory
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	217 with tarfile.open('tmp_data.tar.gz', 'r:gz') as fh:
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	218 for member in fh.getmembers():
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	219 if member.isreg():
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	220 member.name = os.path.basename(member.name)
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	221 fh.extract(member, os.path.join(target_directory, database_path))
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	222
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	223 data_table_entry = {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	224 'data_tables': {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	225 data_table_name: [
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	226 {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	227 "value": database_value,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	228 "name": database_name,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	229 "path": database_path,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	230 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	231 ]
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	232 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	233 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	234
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	235 return data_table_entry
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	236
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	237
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	238 def kraken2_build_special(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	239
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	240 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	241
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	242 special_database_names = {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	243 "rdp": "RDP",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	244 "greengenes": "Greengenes",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	245 "silva": "Silva",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	246 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	247
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	248 database_value = "_".join([
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	249 now,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	250 kraken2_args["special_database_type"],
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	251 "kmer-len", str(kraken2_args["kmer_len"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	252 "minimizer-len", str(kraken2_args["minimizer_len"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	253 "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
4 0eebe086fd58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e" iuc parents: 3 diff changeset	254 "load-factor", str(kraken2_args["load_factor"]),
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	255 ])
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	256
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	257 database_name = " ".join([
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	258 special_database_names[kraken2_args["special_database_type"]],
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	259 "(Created:",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	260 now + ",",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	261 "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	262 "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	263 "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
4 0eebe086fd58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e" iuc parents: 3 diff changeset	264 "load-factor=" + str(kraken2_args["load_factor"]) + ")",
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	265 ])
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	266
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	267 database_path = database_value
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	268
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	269 args = [
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	270 '--threads', str(kraken2_args["threads"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	271 '--special', kraken2_args["special_database_type"],
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	272 '--kmer-len', str(kraken2_args["kmer_len"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	273 '--minimizer-len', str(kraken2_args["minimizer_len"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	274 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
4 0eebe086fd58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e" iuc parents: 3 diff changeset	275 '--load-factor', str(kraken2_args["load_factor"]),
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	276 '--db', database_path
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	277 ]
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	278
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	279 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	280
1 6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	281 if kraken2_args["clean"]:
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	282 args = [
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	283 '--threads', str(kraken2_args["threads"]),
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	284 '--clean',
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	285 '--db', database_path
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	286 ]
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	287
1 6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	288 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	289
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	290 data_table_entry = {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	291 'data_tables': {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	292 data_table_name: [
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	293 {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	294 "value": database_value,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	295 "name": database_name,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	296 "path": database_path,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	297 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	298 ]
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	299 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	300 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	301
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	302 return data_table_entry
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	303
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	304
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	305 def kraken2_build_custom(kraken2_args, custom_database_name, target_directory, data_table_name=DATA_TABLE_NAME):
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	306
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	307 args = [
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	308 '--threads', str(kraken2_args["threads"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	309 '--download-taxonomy',
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	310 '--db', custom_database_name,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	311 ]
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	312
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	313 if kraken2_args['skip_maps']:
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	314 args.append('--skip-maps')
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	315
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	316 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	317
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	318 args = [
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	319 '--threads', str(kraken2_args["threads"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	320 '--add-to-library', kraken2_args["custom_fasta"],
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	321 '--db', custom_database_name
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	322 ]
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	323
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	324 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	325
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	326 args = [
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	327 '--threads', str(kraken2_args["threads"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	328 '--build',
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	329 '--kmer-len', str(kraken2_args["kmer_len"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	330 '--minimizer-len', str(kraken2_args["minimizer_len"]),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	331 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
4 0eebe086fd58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e" iuc parents: 3 diff changeset	332 '--load-factor', str(kraken2_args["load_factor"]),
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	333 '--db', custom_database_name
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	334 ]
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	335
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	336 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	337
1 6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	338 if kraken2_args["clean"]:
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	339 args = [
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	340 '--threads', str(kraken2_args["threads"]),
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	341 '--clean',
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	342 '--db', custom_database_name
6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	343 ]
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	344
1 6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	345 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	346
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	347 data_table_entry = {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	348 'data_tables': {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	349 data_table_name: [
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	350 {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	351 "value": custom_database_name,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	352 "name": custom_database_name,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	353 "path": custom_database_name
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	354 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	355 ]
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	356 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	357 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	358
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	359 return data_table_entry
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	360
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	361
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	362 def main():
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	363 parser = argparse.ArgumentParser()
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	364 parser.add_argument('data_manager_json')
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	365 parser.add_argument('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length')
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	366 parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length')
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	367 parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
4 0eebe086fd58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e" iuc parents: 3 diff changeset	368 parser.add_argument('--load-factor', dest='load_factor', type=float, default=0.7, help='load factor')
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	369 parser.add_argument('--threads', dest='threads', default=1, help='threads')
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	370 parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build')
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	371 parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)')
5 2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	372 parser.add_argument('--standard-prebuilt-size', dest='standard_prebuilt_size', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Size of standard prebuilt database to download (only applies to --database-type standard_prebuilt. Options are: "8", "16", "full".)')
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	373 parser.add_argument('--prebuilt-date', dest='prebuilt_date', help='Database build date (YYYY-MM-DD). Only applies to --database-type standard_prebuilt.')
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	374 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)')
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	375 parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)')
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	376 parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)')
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	377 parser.add_argument('--skip-maps', dest='skip_maps', action='store_true', help='')
1 6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	378 parser.add_argument('--clean', dest='clean', action='store_true', help='Clean up extra files')
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	379 args = parser.parse_args()
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	380
3 19b6a2f0dbe2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165" iuc parents: 2 diff changeset	381 with open(args.data_manager_json) as fh:
19b6a2f0dbe2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165" iuc parents: 2 diff changeset	382 data_manager_input = json.load(fh)
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	383
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	384 target_directory = data_manager_input['output_data'][0]['extra_files_path']
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	385
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	386 try:
3 19b6a2f0dbe2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165" iuc parents: 2 diff changeset	387 os.mkdir(target_directory)
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	388 except OSError as exc:
3 19b6a2f0dbe2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165" iuc parents: 2 diff changeset	389 if exc.errno == errno.EEXIST and os.path.isdir(target_directory):
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	390 pass
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	391 else:
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	392 raise
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	393
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	394 data_manager_output = {}
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	395
5 2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	396 if str(args.database_type) == 'standard_local_build':
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	397 kraken2_args = {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	398 "kmer_len": args.kmer_len,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	399 "minimizer_len": args.minimizer_len,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	400 "minimizer_spaces": args.minimizer_spaces,
4 0eebe086fd58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e" iuc parents: 3 diff changeset	401 "load_factor": args.load_factor,
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	402 "threads": args.threads,
1 6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	403 "clean": args.clean,
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	404 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	405 data_manager_output = kraken2_build_standard(
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	406 kraken2_args,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	407 target_directory,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	408 )
5 2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	409 elif str(args.database_type) == 'standard_prebuilt':
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	410 data_manager_output = kraken2_build_standard_prebuilt(
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	411 str(args.standard_prebuilt_size),
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	412 str(args.prebuilt_date),
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	413 target_directory
2f27f3b86827 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66" iuc parents: 4 diff changeset	414 )
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	415 elif str(args.database_type) == 'minikraken':
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	416 data_manager_output = kraken2_build_minikraken(
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	417 str(args.minikraken2_version),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	418 target_directory
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	419 )
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	420 elif str(args.database_type) == 'special':
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	421 kraken2_args = {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	422 "special_database_type": str(args.special_database_type),
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	423 "kmer_len": args.kmer_len,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	424 "minimizer_len": args.minimizer_len,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	425 "minimizer_spaces": args.minimizer_spaces,
4 0eebe086fd58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e" iuc parents: 3 diff changeset	426 "load_factor": args.load_factor,
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	427 "threads": args.threads,
1 6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	428 "clean": args.clean,
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	429 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	430 data_manager_output = kraken2_build_special(
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	431 kraken2_args,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	432 target_directory,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	433 )
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	434 elif str(args.database_type) == 'custom':
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	435 kraken2_args = {
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	436 "custom_fasta": args.custom_fasta,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	437 "skip_maps": args.skip_maps,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	438 "kmer_len": args.kmer_len,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	439 "minimizer_len": args.minimizer_len,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	440 "minimizer_spaces": args.minimizer_spaces,
4 0eebe086fd58 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e" iuc parents: 3 diff changeset	441 "load_factor": args.load_factor,
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	442 "threads": args.threads,
1 6ba1ec5f86fc planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be iuc parents: 0 diff changeset	443 "clean": args.clean,
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	444 }
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	445 data_manager_output = kraken2_build_custom(
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	446 kraken2_args,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	447 args.custom_database_name,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	448 target_directory,
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	449 )
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	450 else:
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	451 sys.exit("Invalid database type")
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	452
3 19b6a2f0dbe2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165" iuc parents: 2 diff changeset	453 with open(args.data_manager_json, 'w') as fh:
19b6a2f0dbe2 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165" iuc parents: 2 diff changeset	454 json.dump(data_manager_output, fh, sort_keys=True)
0 e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	455
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	456
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	457 if __name__ == "__main__":
e4cdf82de430 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2 iuc parents: diff changeset	458 main()

Mercurial > repos > iuc > data_manager_build_kraken2_database

annotate data_manager/kraken2_build_database.py @ 5:2f27f3b86827 draft