From 6d0e383a602f76a070a31457c0ba0aeca3171642 Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 2 May 2013 09:28:40 -0400 Subject: [PATCH 1/2] Fixing the bundle script 1. someone out there busted it when adding high confidence 1000G calls 2. new path to NA12878 bam 3. updated clashing version argument --- .../sting/queue/qscripts/GATKResourcesBundle.scala | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala index 55e56889a..ad83ac723 100644 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala @@ -40,8 +40,8 @@ class GATKResourcesBundle extends QScript { @Argument(doc="liftOverPerl", required=false) var liftOverPerl: File = new File("./public/perl/liftOverVCF.pl") - @Argument(shortName = "ver", doc="The SVN version of this release", required=true) - var VERSION: String = _ + @Argument(shortName = "ver", doc="The GIT version of this release", required=true) + var BUNDLE_VERSION: String = _ @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") @@ -57,8 +57,8 @@ class GATKResourcesBundle extends QScript { val SITES_EXT: String = "sites" - def BUNDLE_DIR: File = BUNDLE_ROOT + "/" + VERSION - def DOWNLOAD_DIR: File = DOWNLOAD_ROOT + "/" + VERSION + def BUNDLE_DIR: File = BUNDLE_ROOT + "/" + BUNDLE_VERSION + def DOWNLOAD_DIR: File = DOWNLOAD_ROOT + "/" + BUNDLE_VERSION // REFERENCES class Reference( val name: String, val file: File ) { } @@ -161,7 +161,7 @@ class GATKResourcesBundle extends QScript { "1000G_phase1.indels", b37, true, false)) 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", "Mills_and_1000G_gold_standard.indels", b37, true, false)) @@ -182,7 +182,7 @@ class GATKResourcesBundle extends QScript { // // 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)) // From f88a964e2cbde0d9017629ae5aaf073c52f3eaae Mon Sep 17 00:00:00 2001 From: Eric Banks Date: Thu, 2 May 2013 10:54:32 -0400 Subject: [PATCH 2/2] Adding .fai file to example fasta since we don't generate it anymore --- public/testdata/exampleFASTA.fasta.fai | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/public/testdata/exampleFASTA.fasta.fai b/public/testdata/exampleFASTA.fasta.fai index 1cc63a5ed..905b3aec5 100644 --- a/public/testdata/exampleFASTA.fasta.fai +++ b/public/testdata/exampleFASTA.fasta.fai @@ -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