Mercurial > repos > dfornika > data_manager_build_kraken2_database
comparison data_manager/kraken2_build_standard.py @ 1:32d04371ed19 draft
planemo upload for repository https://github.com/dfornika/galaxytools/tree/master/data_managers/data_manager_build_kraken2_database/ commit f05f93ee024df8b38efa1c92db9785d52c726f85-dirty
author | dfornika |
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date | Thu, 28 Feb 2019 13:59:33 -0500 |
parents | 7e43f66abe9d |
children | 1f6fe9dc5490 |
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0:7e43f66abe9d | 1:32d04371ed19 |
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25 '--kmer-len', str(kraken2_args["kmer_len"]), | 25 '--kmer-len', str(kraken2_args["kmer_len"]), |
26 '--minimizer-len', str(kraken2_args["minimizer_len"]), | 26 '--minimizer-len', str(kraken2_args["minimizer_len"]), |
27 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), | 27 '--minimizer-spaces', str(kraken2_args["minimizer_spaces"]), |
28 '--db', database_name | 28 '--db', database_name |
29 ] | 29 ] |
30 pprint(args) | |
31 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory) | 30 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory) |
32 return_code = proc.wait() | 31 return_code = proc.wait() |
33 if return_code: | 32 if return_code: |
34 print("Error building database.", file=sys.stderr) | 33 print("Error building database.", file=sys.stderr) |
35 sys.exit( return_code ) | 34 sys.exit( return_code ) |
36 | 35 args = [ |
36 'kraken2-build', | |
37 '--threads', str(kraken2_args["threads"]), | |
38 '--clean', | |
39 '--db', database_name | |
40 ] | |
41 proc = subprocess.Popen(args=args, shell=False, cwd=target_directory) | |
42 return_code = proc.wait() | |
43 if return_code: | |
44 print("Error building database.", file=sys.stderr) | |
45 sys.exit( return_code ) | |
37 data_table_entry = { | 46 data_table_entry = { |
38 "value": database_name, | 47 "value": database_name, |
39 "name": database_name, | 48 "name": database_name, |
40 "path": database_name | 49 "path": database_name |
41 } | 50 } |