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Hacky fix for LSF confusion -- submitted jobs check to see if their directory exists, despite depending on the job which creates said directory. Filter strings now have escaped quotes. 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3903 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl 2010-07-29 21:35:50 +00:00
parent 0f9baa2e94
commit 54d93f63d2
2 changed files with 9 additions and 1 deletions
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2
scala/qscript/fullCallingPipeline.q
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@ -284,7 +284,7 @@ def endToEnd(base: String, snps: UnifiedGenotyper, indels: UnifiedGenotyperIndel
handFilter.unfilteredVCF = annotated.annotatedVCF handFilter.unfilteredVCF = annotated.annotatedVCF
handFilter.indelMask = indels.indelVCF handFilter.indelMask = indels.indelVCF
handFilter.filterNames = List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun") handFilter.filterNames = List("StrandBias","AlleleBalance","QualByDepth","HomopolymerRun")
handFilter.filterExpressions = List("SB>=0.10","AB>=0.75","QD<5","HRun>=4") handFilter.filterExpressions = List("\"SB>=0.10\"","\"AB>=0.75\"","QD<5","\"HRun>=4\"")
handFilter.filteredVCF = swapExt(annotated.annotatedVCF,".vcf",".handfiltered.vcf") handFilter.filteredVCF = swapExt(annotated.annotatedVCF,".vcf",".handfiltered.vcf")
// 3.i generate gaussian clusters on the masked vcf // 3.i generate gaussian clusters on the masked vcf
val clusters = new GenerateVariantClusters val clusters = new GenerateVariantClusters

8
scala/src/org/broadinstitute/sting/queue/function/scattergather/CreateTempDirsFunction.scala
View File

@ -14,5 +14,13 @@ class CreateTempDirsFunction extends CommandLineFunction {
@Input(doc="Sleep seconds", required=false) @Input(doc="Sleep seconds", required=false)
var mkdirSleepSeconds: Option[Int] = None var mkdirSleepSeconds: Option[Int] = None
// TODO: After port of LSF submitter use -cwd <dir> instead of trying to run from the directory
// For now, create the directory so that BroadCore can run bsub from it -kshakir July 27, 2010 on chartl's computer
override def freeze = {
super.freeze
tempDirectories.foreach(_.mkdirs)
}
def commandLine = "mkdir -pv%s%s".format(repeat(" '", tempDirectories, "'"), optional(" && sleep ", mkdirSleepSeconds)) def commandLine = "mkdir -pv%s%s".format(repeat(" '", tempDirectories, "'"), optional(" && sleep ", mkdirSleepSeconds))
} }