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Merged bug fix from Stable into Unstable

This commit is contained in:
Ryan Poplin 2011-08-08 12:36:17 -04:00
parent 0db79207e8 8072bd9831
commit 99e3a72343
1 changed files with 10 additions and 10 deletions
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20
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
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@ -13,7 +13,7 @@ class GATKResourcesBundle extends QScript {
var gatkJarFile: File = new File("dist/GenomeAnalysisTK.jar") var gatkJarFile: File = new File("dist/GenomeAnalysisTK.jar")
@Argument(doc="liftOverPerl", required=false) @Argument(doc="liftOverPerl", required=false)
var liftOverPerl: File = new File("./perl/liftOverVCF.pl") var liftOverPerl: File = new File("./public/perl/liftOverVCF.pl")
@Argument(shortName = "ver", doc="The SVN version of this release", required=true) @Argument(shortName = "ver", doc="The SVN version of this release", required=true)
var VERSION: String = _ var VERSION: String = _
@ -57,11 +57,11 @@ class GATKResourcesBundle extends QScript {
//Console.printf("liftover(%s => %s)%n", inRef.name, outRef.name) //Console.printf("liftover(%s => %s)%n", inRef.name, outRef.name)
(inRef.name, outRef.name) match { (inRef.name, outRef.name) match {
case ("b37", "hg19") => case ("b37", "hg19") =>
return new LiftOverPerl(in, out, new File("chainFiles/b37tohg19.chain"), inRef, outRef) return new LiftOverPerl(in, out, new File("public/chainFiles/b37tohg19.chain"), inRef, outRef)
case ("b37", "hg18") => case ("b37", "hg18") =>
return new LiftOverPerl(in, out, new File("chainFiles/b37tohg18.chain"), inRef, outRef) return new LiftOverPerl(in, out, new File("public/chainFiles/b37tohg18.chain"), inRef, outRef)
case ("b37", "b36") => case ("b37", "b36") =>
return new LiftOverPerl(in, out, new File("chainFiles/b37tob36.chain"), inRef, outRef) return new LiftOverPerl(in, out, new File("public/chainFiles/b37tob36.chain"), inRef, outRef)
case _ => return null case _ => return null
} }
} }
@ -85,7 +85,7 @@ class GATKResourcesBundle extends QScript {
// //
b37 = new Reference("b37", new File("/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta")) b37 = new Reference("b37", new File("/Users/depristo/Desktop/broadLocal/localData/human_g1k_v37.fasta"))
hg18 = new Reference("hg18", new File("/Users/depristo/Desktop/broadLocal/localData/Homo_sapiens_assembly18.fasta")) hg18 = new Reference("hg18", new File("/Users/depristo/Desktop/broadLocal/localData/Homo_sapiens_assembly18.fasta"))
exampleFASTA = new Reference("exampleFASTA", new File("testdata/exampleFASTA.fasta")) exampleFASTA = new Reference("exampleFASTA", new File("public/testdata/exampleFASTA.fasta"))
refs = List(b37, hg18, exampleFASTA) refs = List(b37, hg18, exampleFASTA)
val DATAROOT = "/Users/depristo/Desktop/broadLocal/localData/" val DATAROOT = "/Users/depristo/Desktop/broadLocal/localData/"
@ -94,7 +94,7 @@ class GATKResourcesBundle extends QScript {
addResource(new Resource(DATAROOT + "dbsnp_132_b37.vcf", "dbsnp_132", b37, true, false)) addResource(new Resource(DATAROOT + "dbsnp_132_b37.vcf", "dbsnp_132", b37, true, false))
addResource(new Resource(exampleFASTA.file, "exampleFASTA", exampleFASTA, false)) addResource(new Resource(exampleFASTA.file, "exampleFASTA", exampleFASTA, false))
addResource(new Resource("testdata/exampleBAM.bam", "exampleBAM", exampleFASTA, false)) addResource(new Resource("public/testdata/exampleBAM.bam", "exampleBAM", exampleFASTA, false))
} }
def initializeStandardDataFiles() = { def initializeStandardDataFiles() = {
@ -105,7 +105,7 @@ class GATKResourcesBundle extends QScript {
b37 = new Reference("b37", new File("/humgen/1kg/reference/human_g1k_v37.fasta")) b37 = new Reference("b37", new File("/humgen/1kg/reference/human_g1k_v37.fasta"))
hg18 = new Reference("hg18", new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta")) hg18 = new Reference("hg18", new File("/seq/references/Homo_sapiens_assembly18/v0/Homo_sapiens_assembly18.fasta"))
b36 = new Reference("b36", new File("/humgen/1kg/reference/human_b36_both.fasta")) b36 = new Reference("b36", new File("/humgen/1kg/reference/human_b36_both.fasta"))
exampleFASTA = new Reference("exampleFASTA", new File("testdata/exampleFASTA.fasta")) exampleFASTA = new Reference("exampleFASTA", new File("public/testdata/exampleFASTA.fasta"))
refs = List(hg19, b37, hg18, b36, exampleFASTA) refs = List(hg19, b37, hg18, b36, exampleFASTA)
addResource(new Resource(b37.file, "", b37, false)) addResource(new Resource(b37.file, "", b37, false))
@ -155,8 +155,8 @@ class GATKResourcesBundle extends QScript {
addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/refGene_b37.sorted.txt", addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/refGene_b37.sorted.txt",
"refGene", b37, true, false)) "refGene", b37, true, false))
addResource(new Resource("chainFiles/hg18tob37.chain", "", hg18, false, false)) addResource(new Resource("public/chainFiles/hg18tob37.chain", "", hg18, false, false))
addResource(new Resource("chainFiles/b36tob37.chain", "", b36, false, false)) addResource(new Resource("public/chainFiles/b36tob37.chain", "", b36, false, false))
// todo -- chain files? // todo -- chain files?
// todo 1000G SNP and indel call sets? // todo 1000G SNP and indel call sets?
@ -165,7 +165,7 @@ class GATKResourcesBundle extends QScript {
// exampleFASTA file // exampleFASTA file
// //
addResource(new Resource(exampleFASTA.file, "exampleFASTA", exampleFASTA, false)) addResource(new Resource(exampleFASTA.file, "exampleFASTA", exampleFASTA, false))
addResource(new Resource("testdata/exampleBAM.bam", "exampleBAM", exampleFASTA, false)) addResource(new Resource("public/testdata/exampleBAM.bam", "exampleBAM", exampleFASTA, false))
} }
def createBundleDirectories(dir: File) = { def createBundleDirectories(dir: File) = {