action='store_true',
help='alignment')
args = parser.parse_args()
if args.verbose:
print "BlockTLScript:", args
if not args.do_sigproc and not args.do_basecalling and not args.do_alignment:
parser.print_help()
sys.exit(1)
#ensure we permit read/write for owner and group output files.
os.umask(0002)
blockprocessing.printheader()
env, warn = explogparser.getparameter()
print warn
blockprocessing.write_version()
sys.stdout.flush()
sys.stderr.flush()
#-------------------------------------------------------------
# Connect to Job Server
#-------------------------------------------------------------
try:
jobserver = xmlrpclib.ServerProxy(
"http://%s:%d" %
(cluster_settings.JOBSERVER_HOST, cluster_settings.JOBSERVER_PORT),
verbose=False,
barcodeSet = env['barcodeId']
runID = env.get('runid', 'ABCDE')
from distutils.sysconfig import get_python_lib
script = os.path.join(get_python_lib(), 'ion', 'reports',
'combineReports_jobs.py')
try:
jobserver = xmlrpclib.ServerProxy("http://%s:%d" %
(JOBSERVER_HOST, JOBSERVER_PORT),
verbose=False,
allow_none=True)
except (socket.error, xmlrpclib.Fault):
traceback.print_exc()
printheader()
primary_key_file = os.path.join(os.getcwd(), 'primary.key')
try:
jobserver.updatestatus(primary_key_file, 'Started', True)
except:
traceback.print_exc()
# Software version
write_version()
# *** Barcodes ***
barcodeSet, barcode_files, barcodeSet_Info = find_barcodes_to_process(
parentBAMs, barcodeSet)
if barcodeSet:
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_zipping:
parser.print_help()
sys.exit(1)
#ensure we permit read/write for owner and group output files.
os.umask(0002)
blockprocessing.printheader()
env,warn = explogparser.getparameter()
blockprocessing.write_version()
sys.stdout.flush()
sys.stderr.flush()
#-------------------------------------------------------------
# Connect to Job Server
#-------------------------------------------------------------
try:
jobserver = xmlrpclib.ServerProxy("http://%s:%d" %
(cluster_settings.JOBSERVER_HOST, cluster_settings.JOBSERVER_PORT),
verbose=False, allow_none=True)
primary_key_file = os.path.join(os.getcwd(),'primary.key')
except:
mark_duplicates = env['mark_duplicates']
override_samples = env.get('override_samples', False)
sample = env.get('sample') or 'none'
barcodeSamples = json.loads(env.get('barcodeSamples','{}'))
barcodeSet = env['barcodeId']
runID = env.get('runid','ABCDE')
from distutils.sysconfig import get_python_lib
script = os.path.join(get_python_lib(), 'ion', 'reports', 'combineReports_jobs.py')
try:
jobserver = xmlrpclib.ServerProxy("http://%s:%d" % (JOBSERVER_HOST, JOBSERVER_PORT), verbose=False, allow_none=True)
except (socket.error, xmlrpclib.Fault):
traceback.print_exc()
printheader()
primary_key_file = os.path.join(os.getcwd(),'primary.key')
try:
jobserver.updatestatus(primary_key_file,'Started',True)
except:
traceback.print_exc()
# Software version
write_version()
# *** Barcodes ***
barcodeSet, barcode_files, barcodeSet_Info = find_barcodes_to_process(parentBAMs, barcodeSet)
if barcodeSet: