Prepare system configuration information from an input configuration file.

    This does the work of parsing the system input file and setting up directories
    for use in 'organize'.

def prep_system(run_info_yaml, bcbio_system=None):
    """Prepare system configuration information from an input configuration file.

    This does the work of parsing the system input file and setting up directories
    for use in 'organize'.
    """
    work_dir = os.getcwd()
    config, config_file = config_utils.load_system_config(bcbio_system, work_dir)
    dirs = setup_directories(work_dir, os.path.normpath(os.path.dirname(os.path.dirname(run_info_yaml))),
                             config, config_file)
    return [dirs, config, run_info_yaml]