Mercurial > repos > dfornika > data_manager_build_kraken2_database

annotate data_manager/kraken2_build_minikraken.py @ 16:d9f190088154 draft

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planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty
author dfornika
date Tue, 05 Mar 2019 16:45:43 -0500
parents 9385ea32f9ac
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
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1 #!/usr/bin/env python
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3 from __future__ import print_function
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5 import argparse
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6 import datetime
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7 import errno
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8 import json
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9 import os
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10 import string
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11 import subprocess
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12 import sys
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15 DATA_TABLE_NAME = "kraken2_databases"
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17 def run(args, cwd):
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18 proc = subprocess.Popen(args=args, shell=False, cwd=cwd)
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19 return_code = proc.wait()
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20 if return_code:
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21 print("Error building database.", file=sys.stderr)
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22 sys.exit( return_code )
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24 def kraken2_build_minikraken(data_manager_dict, minikraken2_version, target_directory, data_table_name=DATA_TABLE_NAME):
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26 now = datetime.datetime.utcnow().strftime("%Y-%m-%dT%H%M%SZ")
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28 database_value = "_".join([
1dc93ae264e6 planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 70494d589aa1990618ebc7a895e91477d41c3203-dirty
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29 now,
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30 "minikraken2",
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31 minikraken2_version,
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32 "8GB",
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33 ])
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35 database_name = " ".join([
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36 "Minikraken2",
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37 minikraken2_version,
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38 "(Created:",
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39 now + ")"
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40 ])
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42 database_path = database_value
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44 args = [
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45 'https://ccb.jhu.edu/software/kraken2/dl/minikraken2_' + minikraken2_version + '_8GB.tgz'
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46 ]
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47
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48 run(['wget'] + args, target_directory)
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50 args = [
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51 '-p',
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52 database_path,
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53 ]
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55 run(['mkdir'] + args, target_directory)
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57 args = [
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58 '-xvzf',
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59 'minikraken2_' + minikraken2_version + '_8GB.tgz',
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60 '-C',
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61 database_path,
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62 ]
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63
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64 run(['tar'] + args, target_directory)
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66 data_table_entry = {
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67 "value": database_value,
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68 "name": database_name,
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69 "path": database_path,
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70 }
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72 _add_data_table_entry(data_manager_dict, data_table_entry)
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75 def _add_data_table_entry(data_manager_dict, data_table_entry, data_table_name=DATA_TABLE_NAME):
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76 data_manager_dict['data_tables'] = data_manager_dict.get( 'data_tables', {} )
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77 data_manager_dict['data_tables'][data_table_name] = data_manager_dict['data_tables'].get( data_table_name, [] )
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78 data_manager_dict['data_tables'][data_table_name].append( data_table_entry )
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79 return data_manager_dict
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80
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81
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82 def main():
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83 parser = argparse.ArgumentParser()
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84 parser.add_argument('data_manager_json')
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85 parser.add_argument( '-v', '--minikraken2-version', dest='minikraken2_version', default="v2", help='MiniKraken2 version (v1 or v2)' )
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86 parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' )
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87
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88 args = parser.parse_args()
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89
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90 data_manager_input = json.loads(open(args.data_manager_json).read())
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91
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92 target_directory = data_manager_input['output_data'][0]['extra_files_path']
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93
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94 try:
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95 os.mkdir( target_directory )
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96 except OSError as exc:
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97 if exc.errno == errno.EEXIST and os.path.isdir( target_directory ):
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98 pass
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99 else:
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100 raise
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101
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102 data_manager_output = {}
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103
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104 kraken2_build_minikraken(
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105 data_manager_output,
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106 args.minikraken2_version,
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107 target_directory,
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108 )
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109
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110 open(args.data_manager_json, 'wb').write(json.dumps(data_manager_output))
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111
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112
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113 if __name__ == "__main__":
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114 main()