comparison data_manager/bowtie2_index_builder.py @ 4:d1d5feb31804 draft

planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/data_managers/data_manager_bowtie2_index_builder commit 5dd2e762b5b84cec1c8344ecbeaf903e7dcc292e

3:83da94c0e4a6

    # TODO: allow multiple FASTA input files
    fasta_base_name = os.path.split( fasta_filename )[-1]
    sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
    os.symlink( fasta_filename, sym_linked_fasta_filename )
    args = [ 'bowtie2-build', sym_linked_fasta_filename, sequence_id ]
    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
    return_code = proc.wait()
    if return_code:
        print("Error building index.", file=sys.stderr)
        sys.exit( return_code )

    # build the index
    build_bowtie2_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES )

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


if __name__ == "__main__":
    main()

4:d1d5feb31804

    # TODO: allow multiple FASTA input files
    fasta_base_name = os.path.split( fasta_filename )[-1]
    sym_linked_fasta_filename = os.path.join( target_directory, fasta_base_name )
    os.symlink( fasta_filename, sym_linked_fasta_filename )
    args = [ 'bowtie2-build', sym_linked_fasta_filename, sequence_id ]
    threads = os.environ.get('GALAXY_SLOTS')
    if threads:
        args.extend(['--threads', threads])
    proc = subprocess.Popen( args=args, shell=False, cwd=target_directory )
    return_code = proc.wait()
    if return_code:
        print("Error building index.", file=sys.stderr)
        sys.exit( return_code )

    # build the index
    build_bowtie2_index( data_manager_dict, options.fasta_filename, params, target_directory, dbkey, sequence_id, sequence_name, data_table_names=options.data_table_name or DEFAULT_DATA_TABLE_NAMES )

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


if __name__ == "__main__":
    main()