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continuing to push to get right answers for long-running jobs 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5054 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2011-01-22 15:02:02 +00:00
parent a50d7f74fa
commit ff61aeb762
2 changed files with 4 additions and 1 deletions
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2
analysis/depristo/distributedGATK/distributedGATKMetrics.py
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@ -32,6 +32,8 @@ def main():
print file, dataset, parallelType, nWays, formatTime(startTime), formatTime(endTime), endToEnd(endTime, startTime), perMSites, runtime print file, dataset, parallelType, nWays, formatTime(startTime), formatTime(endTime), endToEnd(endTime, startTime), perMSites, runtime
def endToEnd(endTime, startTime): def endToEnd(endTime, startTime):
if endTime < startTime:
endTime = endTime + datetime.timedelta(1)
#print 'endToEnd', endTime, startTime #print 'endToEnd', endTime, startTime
return total_minutes(endTime - startTime) return total_minutes(endTime - startTime)

3
analysis/depristo/distributedGATK/runqueue.csh
View File

@ -1,9 +1,10 @@
#!/bin/tcsh #!/bin/tcsh
setenv CMD "java -Djava.io.tmpdir=/broad/shptmp/depristo/tmp -jar /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTKFromLaptop/trunk/dist/Queue.jar -statusTo depristo -S /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTKFromLaptop/trunk/scala/qscript/oneoffs/depristo/distributedGATKPerformance.scala -bsub --gatkjarfile /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTKFromLaptop/trunk/dist/GenomeAnalysisTK.jar -dataset HiSeq $argv[2-$#argv]" setenv CMD "java -Djava.io.tmpdir=/broad/shptmp/depristo/tmp -jar /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTKFromLaptop/trunk/dist/Queue.jar -statusTo depristo -S /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTKFromLaptop/trunk/analysis/depristo/distributedGATK/distributedGATKPerformance.scala -bsub --gatkjarfile /humgen/gsa-scr1/depristo/dev/GenomeAnalysisTKFromLaptop/trunk/dist/GenomeAnalysisTK.jar -dataset HiSeq $argv[2-$#argv]"
if ( $1 == 1 ) then if ( $1 == 1 ) then
pushd short; $CMD -jobQueue hour -run & pushd short; $CMD -jobQueue hour -run &
else if ( $1 == 2 ) then
pushd long; $CMD -jobQueue gsa -long -run & pushd long; $CMD -jobQueue gsa -long -run &
else else
$CMD $CMD