def submit(self):
if self.jobs:
print 'There is already a run with the name "'+self.jobname+'". Exiting...'
sys.exit(1)
# uploading input file once, so we don't need to do it for every job again and again
fm.cp(self.filepath, 'gsiftp://pan.nesi.org.nz/~/inputfiles/'+self.jobname, True)
for i in range(0,self.runs):
# create the job object
job = JobObject(si);
# set a unique jobname
number = str(i+1).zfill(4)
job.setUniqueJobname(self.jobname+"_run_"+number)
# set the commandline that needs to be executed
job.setCommandline(megabeast_path+' '+remote_home_dir+'/inputfiles/'+self.jobname+'/'+self.filename)
job.setSubmissionLocation('pan:pan.nesi.org.nz')
job.setCpus(self.cpus)
job.setWalltime(self.walltime)
job.setMemory(self.memory)
job.setApplication('UltraBEAST')
job.setApplicationVersion('0.1')
#job.addInputFileUrl(self.filepath)
# create the job on the backend and specify the VO to use
temp_jobname = job.createJob("/nz/nesi")
print "created job: '"+temp_jobname+"', submitting..."
# submit the job
job.submitJob()
print "submission finished: " + temp_jobname
%s
"""
if group == '':
group = DEFAULT_GROUP
if queue == '':
queue = DEFAULT_QUEUE
for f in sys.argv[8:]:
input_files.append(f)
try:
job = JobObject(si)
job.setSubmissionLocation(queue)
job.setTimestampJobname("galaxy_" + galaxy_job_id)
job.setMemory(DEFAULT_MEMORY)
job.setWalltimeInSeconds(DEFAULT_WALLTIME)
# stop annoying stats from being written to stderr
job.addEnvironmentVariable("SUPPRESS_STATS", "true")
#create the job script#
except:
print "Cannot setup the job environment"
sys.exit(-4)
#create nesi job_script
try:
# save jobname for job
njn = open(jobname_file, "w")
