Example #1
0
    parser.add_argument('-b', '--do-basecalling', dest='do_basecalling', action='store_true', help='base calling')
    parser.add_argument('-a', '--do-alignment', dest='do_alignment', action='store_true', help='alignment')
    parser.add_argument('-z', '--do-zipping', dest='do_zipping', action='store_true', help='zipping')

    args = parser.parse_args()

    if args.verbose:
        print "MergeTLScript:",args
 
    if not args.do_sigproc and not args.do_basecalling and not args.do_alignment and not args.do_zipping:
        parser.print_help()
        sys.exit(1)


    blockprocessing.printheader()
    env = blockprocessing.getparameter()

    blockprocessing.write_version()
    sys.stdout.flush()
    sys.stderr.flush()

    blocks = blockprocessing.getBlocksFromExpLog(env['exp_json'], excludeThumbnail=True)
    dirs = ['block_%s' % block['id_str'] for block in blocks]


    if args.do_sigproc:

        sigproc.mergeSigProcResults(
            dirs,
            env['pathToRaw'],
            env['skipchecksum'],
Example #2
0
    parser.add_argument('param', default='paramfile', help='param file')

    args = parser.parse_args()

    args.verbose = True
    if args.verbose:
        print "args:",args


    try:
        jobserver = xmlrpclib.ServerProxy("http://%s:%d" % (JOBSERVER_HOST, JOBSERVER_PORT), verbose=False, allow_none=True)
    except (socket.error, xmlrpclib.Fault):
        traceback.print_exc()

    blockprocessing.printheader()
    env = blockprocessing.getparameter()


    try:
        jobserver.updatestatus(os.path.join(os.getcwd(),'primary.key'),'Started',True)
    except:
        traceback.print_exc()


    if args.verbose:
        print env['pe_forward']
        print env['pe_reverse']

    blockprocessing.initreports(env['SIGPROC_RESULTS'], env['BASECALLER_RESULTS'], env['ALIGNMENT_RESULTS'])
    blockprocessing.write_version()