Mercurial > repos > iuc > data_manager_build_kraken2_database

annotate data_manager/kraken2_build_database.py @ 6:691a1055a112 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
author iuc
date Fri, 24 Jun 2022 12:44:01 +0000
parents 0d6cdde238ba
children ba981d05e216
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a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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1 #!/usr/bin/env python
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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3 from __future__ import print_function
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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5 import argparse
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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6 import datetime
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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7 import errno
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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8 import json
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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9 import os
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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10 import shutil
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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11 import subprocess
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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12 import sys
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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13 import tarfile
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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14 from enum import Enum
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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16 try:
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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17 # Python3
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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18 from urllib.request import urlopen
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0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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19 from urllib.error import URLError
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20 except ImportError:
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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21 from urllib2 import urlopen
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0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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22 from urllib2 import URLError
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25 DATA_TABLE_NAME = "kraken2_databases"
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a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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28 class KrakenDatabaseTypes(Enum):
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0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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29 standard_local_build = 'standard_local_build'
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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30 standard_prebuilt = 'standard_prebuilt'
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31 minikraken = 'minikraken'
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32 special = 'special'
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33 custom = 'custom'
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34
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35 def __str__(self):
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36 return self.value
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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39 class SpecialDatabaseTypes(Enum):
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40 rdp = 'rdp'
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41 greengenes = 'greengenes'
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42 silva = 'silva'
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44 def __str__(self):
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45 return self.value
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47
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48 class Minikraken2Versions(Enum):
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49 v1 = 'v1'
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50 v2 = 'v2'
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52 def __str__(self):
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53 return self.value
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55
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56 class StandardPrebuiltSizes(Enum):
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57 viral = "viral"
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58 minusb = "minusb"
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59 standard = "standard"
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60 standard_08gb = "standard_08gb"
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61 standard_16gb = "standard_16gb"
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62 pluspf = "pluspf"
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63 pluspf_08gb = "pluspf_08gb"
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64 pluspf_16gb = "pluspf_16gb"
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65 pluspfp = "pluspfp"
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66 pluspfp_08gb = "pluspfp_08gb"
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67 pluspfp_16gb = "pluspfp_16gb"
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69 def __str__(self):
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70 return self.value
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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72
0
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73 def kraken2_build_standard(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
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74 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
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75
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76 database_value = "_".join([
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77 now,
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78 "standard",
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79 "kmer-len", str(kraken2_args["kmer_len"]),
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80 "minimizer-len", str(kraken2_args["minimizer_len"]),
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81 "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
4
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82 "load-factor", str(kraken2_args["load_factor"]),
0
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83 ])
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84
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85 database_name = " ".join([
5
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86 "Standard (Local Build)",
0
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87 "(Created:",
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88 now + ",",
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89 "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
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90 "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
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91 "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
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92 "load-factor", str(kraken2_args["load_factor"]),
0
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93 ])
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94
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95 database_path = database_value
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96
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97 args = [
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98 '--threads', str(kraken2_args["threads"]),
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99 '--standard',
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100 '--kmer-len', str(kraken2_args["kmer_len"]),
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101 '--minimizer-len', str(kraken2_args["minimizer_len"]),
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102 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
4
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103 '--load-factor', str(kraken2_args["load_factor"]),
0
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104 '--db', database_path
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105 ]
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106
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107 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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108
1
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109 if kraken2_args["clean"]:
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110 args = [
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111 '--threads', str(kraken2_args["threads"]),
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112 '--clean',
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113 '--db', database_path
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114 ]
0
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115
1
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116 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
0
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117
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118 data_table_entry = {
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119 'data_tables': {
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120 data_table_name: [
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121 {
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122 "value": database_value,
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123 "name": database_name,
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124 "path": database_path,
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125 }
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126 ]
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127 }
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128 }
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129
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130 return data_table_entry
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131
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132
6
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133 def kraken2_build_standard_prebuilt(prebuilt_db, prebuilt_date, target_directory, data_table_name=DATA_TABLE_NAME):
5
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134
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135 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
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136
6
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137 prebuild_name = {
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138 'viral': "Viral",
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139 'minusb': "MinusB (archaea, viral, plasmid, human, UniVec_Core)",
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140 'standard': "Standard-Full (archaea, bacteria, viral, plasmid, human,UniVec_Core)",
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141 'standard_08gb': "Standard-8 (Standard with DB capped at 8 GB)",
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142 'standard_16gb': "Standard-16 (Standard with DB capped at 16 GB)",
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143 'pluspf': "PlusPF (Standard plus protozoa and fungi)",
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144 'pluspf_08gb': "PlusPF-8 (PlusPF with DB capped at 8 GB)",
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145 'pluspf_16gb': "PlusPF-16 (PlusPF with DB capped at 16 GB)",
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146 'pluspfp': "PlusPFP (Standard plus protozoa, fungi and plant)",
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147 'pluspfp_08gb': "PlusPFP-8 (PlusPFP with DB capped at 8 GB)",
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148 'pluspfp_16gb': "PlusPFP-16 (PlusPFP with DB capped at 16 GB)"
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149 }
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150
5
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151 database_value = "_".join([
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152 now,
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153 "standard_prebuilt",
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154 prebuilt_db,
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155 prebuilt_date
5
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156 ])
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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157
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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158 database_name = " ".join([
6
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159 "Prebuilt Refseq indexes: ",
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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160 prebuild_name[prebuilt_db],
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161 "(Version: ",
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162 prebuilt_date,
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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163 "- Downloaded:",
5
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164 now + ")"
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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165 ])
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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166
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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167 database_path = database_value
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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168
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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169 # we may need to let the user choose the date when new DBs are posted.
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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170 date_url_str = prebuilt_date.replace('-', '')
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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171 # download the pre-built database
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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172 try:
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
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173 download_url = 'https://genome-idx.s3.amazonaws.com/kraken/k2_%s_%s.tar.gz' % (prebuilt_db, date_url_str)
5
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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174 src = urlopen(download_url)
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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175 except URLError as e:
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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176 print('url: ' + download_url, file=sys.stderr)
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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177 print(e, file=sys.stderr)
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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178 exit(1)
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179
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180 with open('tmp_data.tar.gz', 'wb') as dst:
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181 shutil.copyfileobj(src, dst)
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182 # unpack the downloaded archive to the target directory
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183 with tarfile.open('tmp_data.tar.gz', 'r:gz') as fh:
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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184 for member in fh.getmembers():
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185 if member.isreg():
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186 member.name = os.path.basename(member.name)
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187 fh.extract(member, os.path.join(target_directory, database_path))
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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188
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189 data_table_entry = {
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190 'data_tables': {
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191 data_table_name: [
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192 {
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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193 "value": database_value,
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194 "name": database_name,
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195 "path": database_path,
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196 }
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197 ]
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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198 }
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199 }
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200
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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201 return data_table_entry
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202
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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203
0
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204 def kraken2_build_minikraken(minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME):
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205
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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206 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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207
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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208 database_value = "_".join([
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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209 now,
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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210 "minikraken2",
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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211 minikraken2_version,
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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212 "8GB",
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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213 ])
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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214
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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215 database_name = " ".join([
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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216 "Minikraken2",
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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217 minikraken2_version,
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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218 "(Created:",
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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219 now + ")"
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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220 ])
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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221
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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222 database_path = database_value
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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223
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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224 # download the minikraken2 data
5
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225 try:
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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226 download_url = 'https://genome-idx.s3.amazonaws.com/kraken/minikraken2_%s_8GB_201904.tgz' % minikraken2_version
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227 src = urlopen(download_url)
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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228 except URLError as e:
0d6cdde238ba "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 648fe4911ce49173697f314d70e63e0de95b7e66"
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229 print('url: ' + download_url, file=sys.stderr)
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230 print(e, file=sys.stderr)
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231 exit(1)
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232
0
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233 with open('tmp_data.tar.gz', 'wb') as dst:
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234 shutil.copyfileobj(src, dst)
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235 # unpack the downloaded archive to the target directory
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236 with tarfile.open('tmp_data.tar.gz', 'r:gz') as fh:
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237 for member in fh.getmembers():
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238 if member.isreg():
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239 member.name = os.path.basename(member.name)
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240 fh.extract(member, os.path.join(target_directory, database_path))
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241
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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242 data_table_entry = {
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243 'data_tables': {
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244 data_table_name: [
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245 {
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246 "value": database_value,
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247 "name": database_name,
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248 "path": database_path,
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249 }
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250 ]
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251 }
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252 }
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253
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254 return data_table_entry
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255
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256
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257 def kraken2_build_special(kraken2_args, target_directory, data_table_name=DATA_TABLE_NAME):
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258
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259 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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260
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261 special_database_names = {
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262 "rdp": "RDP",
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263 "greengenes": "Greengenes",
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264 "silva": "Silva",
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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265 }
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266
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267 database_value = "_".join([
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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268 now,
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269 kraken2_args["special_database_type"],
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270 "kmer-len", str(kraken2_args["kmer_len"]),
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271 "minimizer-len", str(kraken2_args["minimizer_len"]),
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272 "minimizer-spaces", str(kraken2_args["minimizer_spaces"]),
4
5f4b0a3cb38b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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273 "load-factor", str(kraken2_args["load_factor"]),
0
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274 ])
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275
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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276 database_name = " ".join([
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277 special_database_names[kraken2_args["special_database_type"]],
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278 "(Created:",
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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279 now + ",",
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280 "kmer-len=" + str(kraken2_args["kmer_len"]) + ",",
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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281 "minimizer-len=" + str(kraken2_args["minimizer_len"]) + ",",
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282 "minimizer-spaces=" + str(kraken2_args["minimizer_spaces"]) + ")",
4
5f4b0a3cb38b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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283 "load-factor=" + str(kraken2_args["load_factor"]) + ")",
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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284 ])
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285
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286 database_path = database_value
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287
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288 args = [
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289 '--threads', str(kraken2_args["threads"]),
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290 '--special', kraken2_args["special_database_type"],
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291 '--kmer-len', str(kraken2_args["kmer_len"]),
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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292 '--minimizer-len', str(kraken2_args["minimizer_len"]),
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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293 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
4
5f4b0a3cb38b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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294 '--load-factor', str(kraken2_args["load_factor"]),
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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295 '--db', database_path
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296 ]
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297
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298 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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299
1
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300 if kraken2_args["clean"]:
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301 args = [
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302 '--threads', str(kraken2_args["threads"]),
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303 '--clean',
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304 '--db', database_path
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305 ]
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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306
1
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307 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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308
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309 data_table_entry = {
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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310 'data_tables': {
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311 data_table_name: [
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312 {
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313 "value": database_value,
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314 "name": database_name,
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315 "path": database_path,
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316 }
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317 ]
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318 }
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319 }
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320
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321 return data_table_entry
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322
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323
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324 def kraken2_build_custom(kraken2_args, custom_database_name, target_directory, data_table_name=DATA_TABLE_NAME):
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325
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326 args = [
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327 '--threads', str(kraken2_args["threads"]),
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328 '--download-taxonomy',
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329 '--db', custom_database_name,
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330 ]
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331
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332 if kraken2_args['skip_maps']:
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333 args.append('--skip-maps')
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334
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335 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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336
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337 args = [
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338 '--threads', str(kraken2_args["threads"]),
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339 '--add-to-library', kraken2_args["custom_fasta"],
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340 '--db', custom_database_name
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341 ]
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342
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343 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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344
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345 args = [
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346 '--threads', str(kraken2_args["threads"]),
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347 '--build',
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348 '--kmer-len', str(kraken2_args["kmer_len"]),
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349 '--minimizer-len', str(kraken2_args["minimizer_len"]),
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350 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]),
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351 '--load-factor', str(kraken2_args["load_factor"]),
0
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352 '--db', custom_database_name
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353 ]
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354
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355 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
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356
1
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357 if kraken2_args["clean"]:
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358 args = [
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359 '--threads', str(kraken2_args["threads"]),
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360 '--clean',
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361 '--db', custom_database_name
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362 ]
0
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363
1
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364 subprocess.check_call(['kraken2-build'] + args, cwd=target_directory)
0
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365
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366 data_table_entry = {
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367 'data_tables': {
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368 data_table_name: [
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369 {
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370 "value": custom_database_name,
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371 "name": custom_database_name,
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372 "path": custom_database_name
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373 }
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374 ]
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375 }
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376 }
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377
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378 return data_table_entry
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379
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380
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381 def main():
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382 parser = argparse.ArgumentParser()
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383 parser.add_argument('data_manager_json')
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384 parser.add_argument('--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length')
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385 parser.add_argument('--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length')
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386 parser.add_argument('--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces')
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387 parser.add_argument('--load-factor', dest='load_factor', type=float, default=0.7, help='load factor')
0
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388 parser.add_argument('--threads', dest='threads', default=1, help='threads')
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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parents:
diff changeset
389 parser.add_argument('--database-type', dest='database_type', type=KrakenDatabaseTypes, choices=list(KrakenDatabaseTypes), required=True, help='type of kraken database to build')
a7c8b9cd05da planemo 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 parser.add_argument('--minikraken2-version', dest='minikraken2_version', type=Minikraken2Versions, choices=list(Minikraken2Versions), help='MiniKraken2 version (only applies to --database-type minikraken)')
6
691a1055a112 planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5d74f13e59c4a2862c108ac1a08c067b0cfb2d97
iuc
parents: 5
diff changeset
391 parser.add_argument('--prebuilt-db', dest='prebuilt_db', type=StandardPrebuiltSizes, choices=list(StandardPrebuiltSizes), help='Prebuilt database to download. Only applies to --database-type standard_prebuilt.')
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0d6cdde238ba "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
392 parser.add_argument('--prebuilt-date', dest='prebuilt_date', help='Database build date (YYYY-MM-DD). Only applies to --database-type standard_prebuilt.')
0
a7c8b9cd05da planemo 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 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)')
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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parents:
diff changeset
394 parser.add_argument('--custom-fasta', dest='custom_fasta', help='fasta file for custom database (only applies to --database-type custom)')
a7c8b9cd05da planemo 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 parser.add_argument('--custom-database-name', dest='custom_database_name', help='Name for custom database (only applies to --database-type custom)')
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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parents:
diff changeset
396 parser.add_argument('--skip-maps', dest='skip_maps', action='store_true', help='')
1
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iuc
parents: 0
diff changeset
397 parser.add_argument('--clean', dest='clean', action='store_true', help='Clean up extra files')
0
a7c8b9cd05da planemo 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 args = parser.parse_args()
a7c8b9cd05da planemo 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
3
4e2adcc98c73 "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
400 with open(args.data_manager_json) as fh:
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iuc
parents: 2
diff changeset
401 data_manager_input = json.load(fh)
0
a7c8b9cd05da planemo 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
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
403 target_directory = data_manager_input['output_data'][0]['extra_files_path']
a7c8b9cd05da planemo 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
a7c8b9cd05da planemo 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 try:
3
4e2adcc98c73 "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
406 os.mkdir(target_directory)
0
a7c8b9cd05da planemo 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 except OSError as exc:
3
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iuc
parents: 2
diff changeset
408 if exc.errno == errno.EEXIST and os.path.isdir(target_directory):
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
409 pass
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
410 else:
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
411 raise
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
412
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
413 data_manager_output = {}
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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parents:
diff changeset
414
5
0d6cdde238ba "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
415 if str(args.database_type) == 'standard_local_build':
0
a7c8b9cd05da planemo 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 kraken2_args = {
a7c8b9cd05da planemo 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 "kmer_len": args.kmer_len,
a7c8b9cd05da planemo 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 "minimizer_len": args.minimizer_len,
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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parents:
diff changeset
419 "minimizer_spaces": args.minimizer_spaces,
4
5f4b0a3cb38b "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit fed92935f1f0b52173d2fddbdd2bbf44e802b51e"
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parents: 3
diff changeset
420 "load_factor": args.load_factor,
0
a7c8b9cd05da planemo 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 "threads": args.threads,
1
5348b6e2823d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be
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parents: 0
diff changeset
422 "clean": args.clean,
0
a7c8b9cd05da planemo 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 }
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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parents:
diff changeset
424 data_manager_output = kraken2_build_standard(
a7c8b9cd05da planemo 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 kraken2_args,
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
426 target_directory,
a7c8b9cd05da planemo 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 )
5
0d6cdde238ba "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
428 elif str(args.database_type) == 'standard_prebuilt':
0d6cdde238ba "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
429 data_manager_output = kraken2_build_standard_prebuilt(
6
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parents: 5
diff changeset
430 str(args.prebuilt_db),
5
0d6cdde238ba "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
431 str(args.prebuilt_date),
0d6cdde238ba "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
432 target_directory
0d6cdde238ba "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
433 )
0
a7c8b9cd05da planemo 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) == 'minikraken':
a7c8b9cd05da planemo 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 data_manager_output = kraken2_build_minikraken(
a7c8b9cd05da planemo 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 str(args.minikraken2_version),
a7c8b9cd05da planemo 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 target_directory
a7c8b9cd05da planemo 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 )
a7c8b9cd05da planemo 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 elif str(args.database_type) == 'special':
a7c8b9cd05da planemo 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 kraken2_args = {
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
441 "special_database_type": str(args.special_database_type),
a7c8b9cd05da planemo 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 "kmer_len": args.kmer_len,
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
443 "minimizer_len": args.minimizer_len,
a7c8b9cd05da planemo 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 "minimizer_spaces": args.minimizer_spaces,
4
5f4b0a3cb38b "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
445 "load_factor": args.load_factor,
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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parents:
diff changeset
446 "threads": args.threads,
1
5348b6e2823d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be
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parents: 0
diff changeset
447 "clean": args.clean,
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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parents:
diff changeset
448 }
a7c8b9cd05da planemo 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 data_manager_output = kraken2_build_special(
a7c8b9cd05da planemo 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 kraken2_args,
a7c8b9cd05da planemo 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 target_directory,
a7c8b9cd05da planemo 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 )
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
453 elif str(args.database_type) == 'custom':
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
454 kraken2_args = {
a7c8b9cd05da planemo 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 "custom_fasta": args.custom_fasta,
a7c8b9cd05da planemo 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 "skip_maps": args.skip_maps,
a7c8b9cd05da planemo 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 "kmer_len": args.kmer_len,
a7c8b9cd05da planemo 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 "minimizer_len": args.minimizer_len,
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
iuc
parents:
diff changeset
459 "minimizer_spaces": args.minimizer_spaces,
4
5f4b0a3cb38b "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
460 "load_factor": args.load_factor,
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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parents:
diff changeset
461 "threads": args.threads,
1
5348b6e2823d planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 5f6f447482ad7e127af78204ffd583c51509a0be
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462 "clean": args.clean,
0
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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463 }
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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464 data_manager_output = kraken2_build_custom(
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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465 kraken2_args,
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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466 args.custom_database_name,
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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467 target_directory,
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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468 )
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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469 else:
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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470 sys.exit("Invalid database type")
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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471
3
4e2adcc98c73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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472 with open(args.data_manager_json, 'w') as fh:
4e2adcc98c73 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
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473 json.dump(data_manager_output, fh, sort_keys=True)
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a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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474
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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475
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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476 if __name__ == "__main__":
a7c8b9cd05da planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_kraken2_database/ commit 30d1a86d5c8a3fa434e24ff915f85f51e514ceb2
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477 main()