Mercurial > repos > dfornika > data_manager_build_kraken2_database
comparison data_manager/kraken2_build_custom.py @ 5:1f6fe9dc5490 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit 47bcc8467200adee842a5574b67bc6ef46c0be71-dirty
author | dfornika |
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date | Mon, 04 Mar 2019 18:59:44 -0500 |
parents | 988c436ad798 |
children |
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4:988c436ad798 | 5:1f6fe9dc5490 |
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21 if return_code: | 21 if return_code: |
22 print("Error building database.", file=sys.stderr) | 22 print("Error building database.", file=sys.stderr) |
23 sys.exit( return_code ) | 23 sys.exit( return_code ) |
24 | 24 |
25 | 25 |
26 def kraken2_build(data_manager_dict, kraken2_args, params, target_directory, data_table_name=DATA_TABLE_NAME): | 26 def kraken2_build(data_manager_dict, kraken2_args, database_name, params, target_directory, data_table_name=DATA_TABLE_NAME): |
27 today = datetime.date.today().isoformat() | 27 today = datetime.date.today().isoformat() |
28 database_name = "_".join([today, "custom"]) | |
29 | 28 |
30 args = [ | 29 args = [ |
31 'kraken2-build', | |
32 '--threads', str(kraken2_args["threads"]), | 30 '--threads', str(kraken2_args["threads"]), |
33 '--download-taxonomy', | 31 '--download-taxonomy', |
34 '--db', database_name | 32 '--db', database_name |
35 ] | 33 ] |
36 | 34 |
37 # run(args, target_directory) | 35 run(['kraken2-build'] + args, target_directory) |
38 | 36 |
39 args = [ | 37 args = [ |
40 'kraken2-build', | |
41 '--threads', str(kraken2_args["threads"]), | 38 '--threads', str(kraken2_args["threads"]), |
42 '--add-to-library', kraken2_args["fasta"], | 39 '--add-to-library', kraken2_args["fasta"], |
43 '--db', database_name | 40 '--db', database_name |
44 ] | 41 ] |
45 | 42 |
46 run(args, target_directory) | 43 run(['kraken2-build'] + args, target_directory) |
47 | 44 |
48 args = [ | 45 args = [ |
49 'kraken2-build', | 46 '--threads', str(kraken2_args["threads"]), |
47 '--build', | |
48 '--kmer-len', str(kraken2_args["kmer_len"]), | |
49 '--minimizer-len', str(kraken2_args["minimizer_len"]), | |
50 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), | |
51 '--db', database_name | |
52 ] | |
53 | |
54 run(['kraken2-build'] + args, target_directory) | |
55 | |
56 args = [ | |
50 '--threads', str(kraken2_args["threads"]), | 57 '--threads', str(kraken2_args["threads"]), |
51 '--clean', | 58 '--clean', |
52 '--db', database_name | 59 '--db', database_name |
53 ] | 60 ] |
54 | 61 |
55 run(args, target_directory) | 62 run(['kraken2-build'] + args, target_directory) |
56 | 63 |
57 data_table_entry = { | 64 data_table_entry = { |
58 "value": database_name, | 65 "value": database_name, |
59 "name": database_name, | 66 "name": database_name, |
60 "path": database_name | 67 "path": database_name |
71 | 78 |
72 | 79 |
73 def main(): | 80 def main(): |
74 parser = argparse.ArgumentParser() | 81 parser = argparse.ArgumentParser() |
75 parser.add_argument('params') | 82 parser.add_argument('params') |
83 parser.add_argument( '-d', '--db', dest='database_name', help='database name' ) | |
76 parser.add_argument( '-k', '--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length' ) | 84 parser.add_argument( '-k', '--kmer-len', dest='kmer_len', type=int, default=35, help='kmer length' ) |
77 parser.add_argument( '-m', '--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length' ) | 85 parser.add_argument( '-m', '--minimizer-len', dest='minimizer_len', type=int, default=31, help='minimizer length' ) |
78 parser.add_argument( '-s', '--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces' ) | 86 parser.add_argument( '-s', '--minimizer-spaces', dest='minimizer_spaces', default=6, help='minimizer spaces' ) |
79 parser.add_argument( '-f', '--fasta', dest='fasta', help='fasta' ) | 87 parser.add_argument( '-f', '--fasta', dest='fasta', help='fasta' ) |
80 parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' ) | 88 parser.add_argument( '-t', '--threads', dest='threads', default=1, help='threads' ) |