Mercurial > repos > iuc > data_manager_bwameth_index_builder
comparison data_manager/bwameth_index_builder.py @ 5:5ab25caa7b7d draft
"planemo upload for repository https://github.com/galaxyproject/tools-iuc/data_managers/data_manager_bwameth_index_builder commit 2c7b238779034cd7b6f459aa972db636af970525"
author | iuc |
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date | Mon, 03 Feb 2020 17:19:38 -0500 |
parents | e7ca32457e36 |
children | fca923910aaa |
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4:a9aa093e2392 | 5:5ab25caa7b7d |
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20 os.symlink(os.path.abspath(args.fasta_filename), sym_linked_fasta_filename) | 20 os.symlink(os.path.abspath(args.fasta_filename), sym_linked_fasta_filename) |
21 cmd = ['bwameth.py', 'index', sym_linked_fasta_filename] | 21 cmd = ['bwameth.py', 'index', sym_linked_fasta_filename] |
22 proc = subprocess.Popen(args=cmd, shell=False, cwd=target_directory) | 22 proc = subprocess.Popen(args=cmd, shell=False, cwd=target_directory) |
23 return_code = proc.wait() | 23 return_code = proc.wait() |
24 if return_code: | 24 if return_code: |
25 print >> sys.stderr, "Error building index." | 25 print("Error building index.", file=sys.stderr) |
26 sys.exit( return_code ) | 26 sys.exit( return_code ) |
27 data_table_entry = dict(value=args.dbkey, dbkey=args.dbkey, name=args.name, path=sym_linked_fasta_filename) | 27 data_table_entry = dict(value=args.dbkey, dbkey=args.dbkey, name=args.name, path=sym_linked_fasta_filename) |
28 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry) | 28 _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry) |
29 | 29 |
30 | 30 |
55 | 55 |
56 # build the index | 56 # build the index |
57 build_bwameth_index(data_manager_dict, params, args) | 57 build_bwameth_index(data_manager_dict, params, args) |
58 | 58 |
59 # save info to json file | 59 # save info to json file |
60 open(filename, 'wb').write(dumps(data_manager_dict)) | 60 open(filename, 'w').write(dumps(data_manager_dict, sort_keys=True)) |
61 | 61 |
62 | 62 |
63 if __name__ == "__main__": | 63 if __name__ == "__main__": |
64 main() | 64 main() |