def _get_system_config(systemconfig, datadir):
    """Retrieve a system configuration with galaxy references specified.
    """
    f = _get_system_configfile(systemconfig, datadir)
    with open(f) as in_handle:
        config = yaml.load(in_handle)
    if "galaxy_config" not in config:
        config["galaxy_config"] = os.path.join(os.path.dirname(f), "universe_wsgi.ini")
    return config
dataset/ETHPy150Open chapmanb/bcbio-nextgen-vm/bcbiovm/docker/run.py/_get_system_config/original