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"

4:a9aa093e2392

    os.symlink(os.path.abspath(args.fasta_filename), sym_linked_fasta_filename)
    cmd = ['bwameth.py', 'index', sym_linked_fasta_filename]
    proc = subprocess.Popen(args=cmd, shell=False, cwd=target_directory)
    return_code = proc.wait()
    if return_code:
        print >> sys.stderr, "Error building index."
        sys.exit( return_code )
    data_table_entry = dict(value=args.dbkey, dbkey=args.dbkey, name=args.name, path=sym_linked_fasta_filename)
    _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)

    # build the index
    build_bwameth_index(data_manager_dict, params, args)

    # save info to json file
    open(filename, 'wb').write(dumps(data_manager_dict))


if __name__ == "__main__":
    main()

5:5ab25caa7b7d

    os.symlink(os.path.abspath(args.fasta_filename), sym_linked_fasta_filename)
    cmd = ['bwameth.py', 'index', sym_linked_fasta_filename]
    proc = subprocess.Popen(args=cmd, shell=False, cwd=target_directory)
    return_code = proc.wait()
    if return_code:
        print("Error building index.", file=sys.stderr)
        sys.exit( return_code )
    data_table_entry = dict(value=args.dbkey, dbkey=args.dbkey, name=args.name, path=sym_linked_fasta_filename)
    _add_data_table_entry(data_manager_dict, data_table_name, data_table_entry)

    # build the index
    build_bwameth_index(data_manager_dict, params, args)

    # save info to json file
    open(filename, 'w').write(dumps(data_manager_dict, sort_keys=True))


if __name__ == "__main__":
    main()