def _read_system_config(dockerconf, systemconfig, datadir):
    config = _get_system_config(systemconfig, datadir)
    # Map external galaxy specifications over to docker container
    dmounts = []
    for k in ["galaxy_config"]:
        if k in config:
            dirname, base = os.path.split(os.path.normpath(os.path.realpath(config[k])))
            dmounts.append("%s:%s" % (dirname, dirname))
            dmounts.extend(mounts.find_genome_directory(dirname))
            config[k] = str(os.path.join(dirname, base))
    return config, dmounts
dataset/ETHPy150Open chapmanb/bcbio-nextgen-vm/bcbiovm/docker/run.py/_read_system_config/original