def manageJob(self, jobFile, baseDir):
#we will want to capture the process exit code and SGE number
jobNumberSGE = -1
#load the job file
jsonData = open(jobFile)
fileData = json.load(jsonData)
#logging.debug('%s - %s' % (getTimestamp(), fileData))
#create the output folder
if 'name' in fileData:
outputFolder = '%s/%s' % (fileData['sample_folder'],
fileData['name'])
else:
outputFolder = fileData['output_folder']
logging.debug('%s - Creating output folder %s' %
(getTimestamp(), outputFolder))
fileData['output_folder'] = outputFolder
#see if it exists first
if not os.path.exists(outputFolder):
os.makedirs(outputFolder)
#write the job template
fileData['json_file'] = jobFile
templateWriter = TemplateWriter(outputFolder, self.__softwareDirectory,
self.__QCSettings, self.__sendEmail)
analysisFile = templateWriter.writeTemplate(fileData)
#now we can pass the job to be executed over to the job runner
runner = Runner("CommandLine")
logging.info('%s - Starting %s' % (getTimestamp(), analysisFile))
fileData['status'] = 'submitted'
fileData['output_folder'] = outputFolder
# if the --requeue option was specified, update the queue
if options.requeue:
fileData['analysis']['settings']['queue'] = options.requeue
# if the user specified a different software directory, set that here
if 'software_directory' not in fileData[
'analysis'] or self.__softwareDirectory != fileData[
'analysis']['software_directory']:
fileData['analysis'][
'software_directory'] = self.__softwareDirectory
#update the json
self.__updateJSON(jobFile, fileData)
#submit the job to SGE
sgeJobID = runner.submitToSGE('%s/job.sh' % (outputFolder), fileData)
fileData['status'] = 'queued'
fileData['sge_job_id'] = sgeJobID
logging.info('%s - Submitted to SGE (%i)' % (getTimestamp(), sgeJobID))
#update the json
self.__updateJSON(jobFile, fileData)
def manageJob(self, jobFile, baseDir):
#we will want to capture the process exit code and SGE number
jobNumberSGE = -1
#load the job file
jsonData = open(jobFile)
fileData = json.load(jsonData)
#logging.debug('%s - %s' % (getTimestamp(), fileData))
#create the output folder
if 'name' in fileData:
outputFolder = '%s/%s' %(fileData['sample_folder'], fileData['name'])
else:
outputFolder = fileData['output_folder']
logging.debug('%s - Creating output folder %s' % (getTimestamp(), outputFolder))
fileData['output_folder'] = outputFolder
#see if it exists first
if not os.path.exists(outputFolder):
os.makedirs(outputFolder)
#write the job template
fileData['json_file'] = jobFile
templateWriter = TemplateWriter(outputFolder, self.__softwareDirectory)
analysisFile = templateWriter.writeTemplate(fileData)
#now we can pass the job to be executed over to the job runner
runner = Runner("CommandLine")
logging.info('%s - Starting %s' % (getTimestamp(), analysisFile))
fileData['status'] = 'submitted'
fileData['output_folder'] = outputFolder
# if the --requeue option was specified, update the queue
if options.requeue:
fileData['analysis']['settings']['queue'] = options.requeue
#update the json
self.__updateJSON(jobFile, fileData)
#submit the job to SGE
sgeJobID = runner.submitToSGE('%s/job.sh' % (outputFolder), fileData)
fileData['status'] = 'queued'
fileData['sge_job_id'] = sgeJobID
logging.info('%s - Submitted to SGE (%i)' % (getTimestamp(), sgeJobID))
#update the json
self.__updateJSON(jobFile, fileData)
def manageJob(self, jobFile, baseDir):
#we will want to capture the process exit code and SGE number
jobNumberSGE = -1
#load the job file
jsonData = open(jobFile)
fileData = json.load(jsonData)
logging.debug('%s - %s' % (getTimestamp(), fileData))
#create the output folder
outputFolder = '%s/%s/%s/%s' % (baseDir, fileData['project'],
fileData['sample'], fileData['name'])
logging.debug('%s - Creating output folder %s' %
(getTimestamp(), outputFolder))
fileData['output_folder'] = outputFolder
#see if it exists first
if not os.path.exists(outputFolder):
os.makedirs(outputFolder)
#write the job template
fileData['json_file'] = jobFile
templateWriter = TemplateWriter(outputFolder, self.__softwareDirectory)
analysisFile = templateWriter.writeTemplate(fileData)
#now we can pass the job to be executed over to the job runner
runner = Runner("CommandLine")
logging.info('%s - Starting %s' % (getTimestamp(), analysisFile))
fileData['status'] = 'submitted'
fileData['output_folder'] = outputFolder
#update the json
self.__updateJSON(jobFile, fileData)
#submit the job to SGE
sgeJobID = runner.submitToSGE('%s/job.sh' % (outputFolder), fileData)
fileData['status'] = 'queued'
fileData['sge_job_id'] = sgeJobID
logging.info('%s - Submitted to SGE (%i)' % (getTimestamp(), sgeJobID))
#update the json
self.__updateJSON(jobFile, fileData)
