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full path to Rscript 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3999 348d0f76-0448-11de-a6fe-93d51630548a
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depristo 2010-08-10 12:02:38 +00:00
parent 9b432d0801
commit cd2d051209
1 changed files with 2 additions and 2 deletions
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4
scala/qscript/recalibrate.scala
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@ -19,7 +19,7 @@ def script = {
val recalData = new File(bamRoot + ".recal_data.csv") val recalData = new File(bamRoot + ".recal_data.csv")
val recalBam = new File(bamRoot + ".recal.bam") val recalBam = new File(bamRoot + ".recal.bam")
val recalRecalData = new File(bamRoot + ".recal.recal_data.csv") val recalRecalData = new File(bamRoot + ".recal.recal_data.csv")
//add(new CountCovariates(root, recalData, "-OQ")) //add(new CountCovariates(bamIn, recalData, "-OQ"))
val tableRecal = new TableRecalibrate(bamIn, recalData, recalBam) { useOriginalQualities = true } val tableRecal = new TableRecalibrate(bamIn, recalData, recalBam) { useOriginalQualities = true }
if ( scatter ) { if ( scatter ) {
tableRecal.intervals = new File("/humgen/gsa-hpprojects/GATK/data/chromosomes.hg18.interval_list") tableRecal.intervals = new File("/humgen/gsa-hpprojects/GATK/data/chromosomes.hg18.interval_list")
@ -69,7 +69,7 @@ class AnalyzeCovariates(recalDataIn: File, outputDir: File) extends org.broadin
this.output_dir = outputDir.toString this.output_dir = outputDir.toString
this.path_to_resources = "/home/radon01/depristo/dev/GenomeAnalysisTK/trunk/R/" this.path_to_resources = "/home/radon01/depristo/dev/GenomeAnalysisTK/trunk/R/"
this.ignoreQ = Some(5) this.ignoreQ = Some(5)
this.path_to_Rscript = "/broad/tools/apps/R-2.6.0/bin/Rscript" this.path_to_Rscript = "/broad/software/free/Linux/redhat_5_x86_64/pkgs/r_2.7.2/bin/Rscript"
this.memoryLimit = Some(4) this.memoryLimit = Some(4)
override def dotString = "AnalyzeCovariates: %s".format(recalDataIn.getName) override def dotString = "AnalyzeCovariates: %s".format(recalDataIn.getName)