

def do_analysis(args, dockerconf):
    'Run a full analysis on a local machine, utilizing multiple cores.\n    '
    work_dir = os.getcwd()
    with open(args.sample_config) as in_handle:
        (sample_config, dmounts) = mounts.update_config(yaml.load(in_handle), args.fcdir)
    dmounts += mounts.prepare_system(args.datadir, dockerconf['biodata_dir'])
    dmounts.append(('%s:%s' % (work_dir, dockerconf['work_dir'])))
    (system_config, system_mounts) = _read_system_config(dockerconf, args.systemconfig, args.datadir)
    system_cfile = os.path.join(work_dir, 'bcbio_system-forvm.yaml')
    sample_cfile = os.path.join(work_dir, 'bcbio_sample-forvm.yaml')
    with open(system_cfile, 'w') as out_handle:
        yaml.dump(system_config, out_handle, default_flow_style=False, allow_unicode=False)
    with open(sample_cfile, 'w') as out_handle:
        yaml.dump(sample_config, out_handle, default_flow_style=False, allow_unicode=False)
    in_files = [os.path.join(dockerconf['work_dir'], os.path.basename(x)) for x in [system_cfile, sample_cfile]]
    log.setup_local_logging({
        'include_time': False,
    })
    manage.run_bcbio_cmd(args.image, (dmounts + dmounts), (in_files + ['--numcores', str(args.numcores), ('--workdir=%s' % dockerconf['work_dir'])]))

dataset/ETHPy150Open chapmanb/bcbio-nextgen-vm/bcbiovm/docker/run.py do_analysis/VarMisuse@254/418 `system_mounts`->`dmounts`