Mercurial > repos > iuc > data_manager_build_bracken_database

annotate data_manager/bracken_build_database.py @ 3:66055e6b3cdf draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
author iuc
date Mon, 08 Nov 2021 15:51:15 +0000
parents 9ddc95bb2220
children
Ignore whitespace changes - Everywhere: Within whitespace: At end of lines:
rev   line source
0
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
1 #!/usr/bin/env python
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
2
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
3 from __future__ import print_function
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
4
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
5 import argparse
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
6 import errno
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
7 import json
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
8 import os
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
9 import subprocess
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
10 import uuid
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
11
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
12
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
13 DATA_TABLE_NAME = "bracken_databases"
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
14
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
15
3
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
16 def bracken_build_database(target_directory, bracken_build_args, database_name, prebuilt=False, data_table_name=DATA_TABLE_NAME):
0
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
17
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
18 database_value = str(uuid.uuid4())
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
19
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
20 database_name = database_name
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
21
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
22 database_path = os.path.join(bracken_build_args['kraken_database'], 'database' + str(bracken_build_args['read_len']) + 'mers.kmer_distrib')
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
23
3
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
24 if not prebuilt:
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
25 bracken_build_args_list = [
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
26 '-t', bracken_build_args['threads'],
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
27 '-k', bracken_build_args['kmer_len'],
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
28 '-l', bracken_build_args['read_len'],
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
29 '-d', bracken_build_args['kraken_database'],
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
30 ]
0
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
31
3
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
32 subprocess.check_call(['bracken-build'] + bracken_build_args_list)
0
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
33
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
34 data_table_entry = {
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
35 "data_tables": {
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
36 data_table_name: [
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
37 {
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
38 "value": database_value,
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
39 "name": database_name,
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
40 "path": database_path,
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
41 }
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
42 ]
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
43 }
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
44 }
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
45
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
46 return data_table_entry
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
47
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
48
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
49 def main():
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
50 parser = argparse.ArgumentParser()
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
51 parser.add_argument('data_manager_json')
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
52 parser.add_argument('--threads', dest='threads', default=1, help='threads')
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
53 parser.add_argument('--kmer-len', dest='kmer_len', help='K-mer length')
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
54 parser.add_argument('--read-len', dest='read_len', help='Read length')
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
55 parser.add_argument('--kraken-db', dest='kraken_database', help='Kraken Database')
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
56 parser.add_argument('--database-name', dest='database_name', help='Database Name')
3
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
57 parser.add_argument('--prebuilt', action='store_true', dest='prebuilt', help='Use pre-built DB')
0
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
58 args = parser.parse_args()
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
59
2
9ddc95bb2220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
parents: 0
diff changeset
60 with open(args.data_manager_json) as fh:
9ddc95bb2220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
parents: 0
diff changeset
61 data_manager_input = json.load(fh)
0
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
62
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
63 target_directory = data_manager_input['output_data'][0]['extra_files_path']
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
64
3
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
65 if args.prebuilt:
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
66 bracken_build_args = {
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
67 'threads': args.threads,
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
68 'read_len': args.read_len,
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
69 'kraken_database': args.kraken_database,
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
70 }
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
71 else:
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
72 bracken_build_args = {
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
73 'threads': args.threads,
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
74 'kmer_len': args.kmer_len,
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
75 'read_len': args.read_len,
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
76 'kraken_database': args.kraken_database,
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
77 }
0
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
78
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
79 try:
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
80 os.mkdir(target_directory)
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
81 except OSError as exc:
2
9ddc95bb2220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
parents: 0
diff changeset
82 if exc.errno == errno.EEXIST and os.path.isdir(target_directory):
0
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
83 pass
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
84 else:
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
85 raise
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
86
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
87 data_manager_output = {}
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
88
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
89 data_manager_output = bracken_build_database(
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
90 target_directory,
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
91 bracken_build_args,
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
92 args.database_name,
3
66055e6b3cdf "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 798f4c97da10258a9ab6c16903b169ce69a05523"
iuc
parents: 2
diff changeset
93 args.prebuilt,
0
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
94 )
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
95
2
9ddc95bb2220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
parents: 0
diff changeset
96 with open(args.data_manager_json, 'w') as fh:
9ddc95bb2220 "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 02d2967f77e3fa5a18aea63dc84aa9ab418dc165"
iuc
parents: 0
diff changeset
97 json.dump(data_manager_output, fh, sort_keys=True)
0
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
98
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
99
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
100 if __name__ == "__main__":
0891b7492a3c "planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_build_bracken_database/ commit 74e81c69c8806d98beb15a889741bcd702866ce3"
iuc
parents:
diff changeset
101 main()