From 54d93f63d2dc7179cd78d017d77e3c1d9a4c6dd0 Mon Sep 17 00:00:00 2001 From: chartl Date: Thu, 29 Jul 2010 21:35:50 +0000 Subject: [PATCH] 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 --- scala/qscript/fullCallingPipeline.q | 2 +- .../function/scattergather/CreateTempDirsFunction.scala | 8 ++++++++ 2 files changed, 9 insertions(+), 1 deletion(-) diff --git a/scala/qscript/fullCallingPipeline.q b/scala/qscript/fullCallingPipeline.q index 138237f5d..2cd3aed45 100755 --- a/scala/qscript/fullCallingPipeline.q +++ b/scala/qscript/fullCallingPipeline.q @@ -284,7 +284,7 @@ def endToEnd(base: String, snps: UnifiedGenotyper, indels: UnifiedGenotyperIndel handFilter.unfilteredVCF = annotated.annotatedVCF handFilter.indelMask = indels.indelVCF 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") // 3.i generate gaussian clusters on the masked vcf val clusters = new GenerateVariantClusters diff --git a/scala/src/org/broadinstitute/sting/queue/function/scattergather/CreateTempDirsFunction.scala b/scala/src/org/broadinstitute/sting/queue/function/scattergather/CreateTempDirsFunction.scala index 1acdc2f75..de1a16652 100644 --- a/scala/src/org/broadinstitute/sting/queue/function/scattergather/CreateTempDirsFunction.scala +++ b/scala/src/org/broadinstitute/sting/queue/function/scattergather/CreateTempDirsFunction.scala @@ -14,5 +14,13 @@ class CreateTempDirsFunction extends CommandLineFunction { @Input(doc="Sleep seconds", required=false) var mkdirSleepSeconds: Option[Int] = None + // TODO: After port of LSF submitter use -cwd 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)) }