From 549172af10bda4db028d407337d0ad7ab73d4aeb Mon Sep 17 00:00:00 2001 From: depristo Date: Fri, 27 May 2011 10:12:09 +0000 Subject: [PATCH] removing dependance on jobQueue == gsa git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5889 348d0f76-0448-11de-a6fe-93d51630548a --- .../oneoffs/depristo/manySampleUGPerformance.scala | 10 +++++----- 1 file changed, 5 insertions(+), 5 deletions(-) diff --git a/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala b/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala index 62c88b6b0..a85928dd2 100755 --- a/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala +++ b/scala/qscript/oneoffs/depristo/manySampleUGPerformance.scala @@ -31,13 +31,13 @@ class ManySampleUGPerformanceTesting extends QScript { this.jarFile = gatkJarFile; this.intervals = List(new File(TARGET_INTERVAL)); this.reference_sequence = referenceFile; - this.jobQueue = "gsa"; - this.memoryLimit = 8 + //this.jobQueue = "gsa"; + this.memoryLimit = 4 //this.commandDirectory = new File("results"); } def script = { - for (nSamples <- if ( EXOME_NSAMPLES) List(1, 2, 4, 8, 16, 32, 60) else List(1, 2, 5, 10, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900) ) { + for (nSamples <- if ( EXOME_NSAMPLES) List(1, 2, 5, 10, 25, 50, 100, 200, 300, 400, 500) else List(1, 2, 5, 10, 50, 100, 200, 300, 400, 500, 600, 700, 800, 900) ) { // for (nSamples <- List(10)) { val sublist = new SliceList(nSamples) val mergeSublist = new MergeBAMs(sublist.list) @@ -69,7 +69,7 @@ class ManySampleUGPerformanceTesting extends QScript { } class Index(bamIn: File) extends SamtoolsIndexFunction { - this.jobQueue = "gsa" + //this.jobQueue = "gsa" bamFile = bamIn } @@ -98,7 +98,7 @@ class ManySampleUGPerformanceTesting extends QScript { class SliceList(n: Int) extends CommandLineFunction { @Output(doc="foo") var list: File = new File("bams.%d.list".format(n)) def commandLine = "head -n %d %s > %s".format(n, FULL_BAM_LIST, list) - this.jobQueue = "gsa"; + //this.jobQueue = "gsa"; } }