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Memory string added 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3771 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-07-12 20:43:19 +00:00
parent 52c534a8f2
commit 80a5ddfa2f
1 changed files with 5 additions and 2 deletions
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7
python/JobDispatcher.py
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@ -10,7 +10,7 @@ import RefseqLibrary
MAX_UNNAMED_DEPENDENCIES = 0
class FarmJob:
def __init__( self, cmd_str_from_user, jobName, projectName, delayTime = None, jobsDependingOnThis = None,
outputFile = None, dependencies = [], dependencyNameString = None, dieOnFail = False, usingFiles = []):
outputFile = None, dependencies = [], dependencyNameString = None, dieOnFail = False, usingFiles = [], memory = None):
self.cmd_str_from_user = cmd_str_from_user
self.jobName = jobName
self.projectName = projectName
@ -36,6 +36,7 @@ class FarmJob:
self.executionString = None # currently unscheduled
self.executed = False
self.jobStatus = None
self.memory = memory.strip("g")
def __hash__(self):
return self.cmd_str_from_user.__hash__()
@ -110,6 +111,8 @@ def buildSubmitString(farmJob,queue):
submitStr += " -b "+delayToGlobalTime(farmJob.delayTime)
if ( farmJob.dependencies != [] ):
submitStr += " -w "+buildDependencyString(farmJob.dependencies)
if ( farmJob.memory != None ):
submitStr += " -R \"rusage[mem="+farmJob.memory+"]\""
submitStr += " "+farmJob.cmd_str_from_user
return submitStr
@ -387,7 +390,7 @@ class GATKDispatcher(JobDispatcher):
intFile.write(interval.bedFormat()+"\n")
intFile.close()
cmd += " -L "+job_dir+"job"+str(num)+"_intervals.interval_list"
job = FarmJob(cmd,self.project+"_job"+str(num),self.project,None,None,job_dir+"bsub_out.txt",list(),None,False,[job_dir+"job"+str(num)+"_intervals.interval_list"])
job = FarmJob(cmd,self.project+"_job"+str(num),self.project,None,None,job_dir+"bsub_out.txt",list(),None,False,[job_dir+"job"+str(num)+"_intervals.interval_list"],self.memory)
return job
def appendOutput(self,command,num,job_dir):