

def _read_system_config(dockerconf, systemconfig, datadir):
    config = _get_system_config(systemconfig, datadir)
    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