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'],
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()