pythonCmd += " --paired_end"
pythonCmd += " --genome {genome}".format(genome=genome)
if force:
pythonCmd += " --force"
pythonCmd += " {controlConf} {sampConf}".format(controlConf=controlConf,sampConf=sampConf)
pythonCmd += " 2> {stderr}".format(stderr=stderr)
logfh.write(pythonCmd + "\n")
qsubCmd = "qsub -V -sync y -wd {sampDir} -m a -M {notifyEmail} {pythonCmd}".format(sampDir=sampDir,notifyEmail=",".join(notifyEmail),pythonCmd=pythonCmd)
logfh.write(qsubCmd)
#
try:
# #set scoring status of ChIP Seq Scoring object in Syapse to "Running Analysis"
# syapseConn = SyapseUtils.Utils(mode=args.syapse_mode)
# syapseConn.setProperty(unique_id=runName,propertyName="scoringStatus",value="Running Analysis") #returns a syapse_client.err.PropertyValueError if value not in property range. returns a syapse_client.err.SemanticConstraintError if the property doesn't belong to the class.
# print(qsubCmd)
stdout,stderr = gbsc_utils.createSubprocess(cmd=qsubCmd,checkRetcode=True)
except Exception as e:
subject = "Chip Scoring {program}: {runName} failed.".format(runName=runName,program=os.path.basename(sys.argv[0]))
body = e.message + "\n\nCheck the SGE log files in " + sampDir + " for more details."
emailCmd = "mandrill_general_email.py --sender {sender} --subject \"{subject}\" --to {notifyEmail} --add \"{body}\" ".format(sender=conf.sender,subject=subject,notifyEmail=" ".join(notifyEmail),body=body)
print(emailCmd)
gbsc_utils.createSubprocess(cmd=emailCmd,checkRetcode=True)
#update Syapse's Chip Seq Scoring object's Scoring Status attribute to 'Running Analysis'
logfh.close()
elif os.path.isdir(i):
shutil.rmtree(i)
# refTime = datetime.datetime(2014,6,20)
# if args.sample_time:
# try:
# mtime = os.path.getmtime(sampleResultsPath)
# except OSError:
# mtime = 0
# if mtime:
# dte = datetime.datetime.fromtimestamp(mtime)
# if dte > refTime:
# print("Continuing")
# continue #assume that scoring is still ongoing
# cmd = "qsub -sync y -wd {wd} -m ae -M {notify} -V runPeakseqWithoutSnapUpdates.rb --name {run} --control {control} --force".format(notify=conf.toEmails[0],wd=sampleRunPath,run=run,control=control)
cmd = "runPeakseqWithoutSnapUpdates.py --syapse-mode {syapseMode} --name {run} --control {control} --force".format(syapseMode=syapseMode,notify=conf.toEmails[0],wd=sampleRunPath,run=run,control=control)
if args.paired_end:
pass #runPeakseqWithoutSnapUpdates.py expects PE by default
if args.rescore_control > 0:
cmd += " --rescore-control={}".format(args.rescore_control)
print(cmd)
#let progam continue if runPeakseqWithoutSnapUpdates.py failes, since an email will already be sent in that case, to the 'sender' specified in conf.py.
try:
popen = gbsc_utils.createSubprocess(cmd=cmd,checkRetcode=False)
except Exception as e:
print(e.message)
if limit:
count += 1
if count >= limit:
break
fh.close()