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Merge pull request #207 from broadinstitute/eb_fixing_bundle_script 

Fixing the bundle script
This commit is contained in:
Mark DePristo 2013-05-02 08:18:19 -07:00
parent 803f666fd5 f88a964e2c
commit dfdc0df4f1
2 changed files with 8 additions and 7 deletions
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12
public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala
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@ -40,8 +40,8 @@ class GATKResourcesBundle extends QScript {
@Argument(doc="liftOverPerl", required=false) @Argument(doc="liftOverPerl", required=false)
var liftOverPerl: File = new File("./public/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 GIT version of this release", required=true)
var VERSION: String = _ var BUNDLE_VERSION: String = _
@Argument(shortName = "bundleDir", doc="Path to root where resource files will be placed", required=false) @Argument(shortName = "bundleDir", doc="Path to root where resource files will be placed", required=false)
val BUNDLE_ROOT = new File("/humgen/gsa-hpprojects/GATK/bundle") val BUNDLE_ROOT = new File("/humgen/gsa-hpprojects/GATK/bundle")
@ -57,8 +57,8 @@ class GATKResourcesBundle extends QScript {
val SITES_EXT: String = "sites" val SITES_EXT: String = "sites"
def BUNDLE_DIR: File = BUNDLE_ROOT + "/" + VERSION def BUNDLE_DIR: File = BUNDLE_ROOT + "/" + BUNDLE_VERSION
def DOWNLOAD_DIR: File = DOWNLOAD_ROOT + "/" + VERSION def DOWNLOAD_DIR: File = DOWNLOAD_ROOT + "/" + BUNDLE_VERSION
// REFERENCES // REFERENCES
class Reference( val name: String, val file: File ) { } class Reference( val name: String, val file: File ) { }
@ -161,7 +161,7 @@ class GATKResourcesBundle extends QScript {
"1000G_phase1.indels", b37, true, false)) "1000G_phase1.indels", b37, true, false))
addResource(new Resource("/humgen/1kg/processing/official_release/phase1/projectConsensus/phase1.wgs.projectConsensus.v2b.recal.highQuality.vcf", addResource(new Resource("/humgen/1kg/processing/official_release/phase1/projectConsensus/phase1.wgs.projectConsensus.v2b.recal.highQuality.vcf",
"1000G_phase1.snps.high_confidence, b37, true, false)) "1000G_phase1.snps.high_confidence", b37, true, false))
addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/GoldStandardIndel/gold.standard.indel.MillsAnd1000G.b37.vcf", addResource(new Resource("/humgen/gsa-hpprojects/GATK/data/Comparisons/Unvalidated/GoldStandardIndel/gold.standard.indel.MillsAnd1000G.b37.vcf",
"Mills_and_1000G_gold_standard.indels", b37, true, false)) "Mills_and_1000G_gold_standard.indels", b37, true, false))
@ -182,7 +182,7 @@ class GATKResourcesBundle extends QScript {
// //
// Test BAM file, specific to each reference // Test BAM file, specific to each reference
// //
addResource(new Resource("/humgen/gsa-hpprojects/NA12878Collection/bams/NA12878.HiSeq.WGS.bwa.cleaned.recal.b37.20.bam", addResource(new Resource("/humgen/gsa-hpprojects/NA12878Collection/bams/CEUTrio.HiSeq.WGS.b37.NA12878.bam",
"IGNORE", b37, false, false)) "IGNORE", b37, false, false))
// //

3
public/testdata/exampleFASTA.fasta.fai vendored
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@ -1 +1,2 @@
chr1 100000 6 60 61 @HD VN:1.4 SO:unsorted
@SQ SN:chr1 LN:100000 UR:file:/humgen/gsa-scr1/ebanks/Sting_unstable/public/testdata/exampleFASTA.fasta M5:b52f0a0422e9544b50ac1f9d2775dc23