From 4080e2cd88c357623ab67944761f2ab3638c4866 Mon Sep 17 00:00:00 2001 From: Mauricio Carneiro Date: Fri, 22 Jul 2011 14:41:22 -0400 Subject: [PATCH] * Added the decoy reference to the bundle under the b37 resources. * Updated the -svn argument to -ver since we don't use svn anymore (also updated the wiki). --- .../sting/queue/qscripts/GATKResourcesBundle.scala | 14 ++++++++++---- 1 file changed, 10 insertions(+), 4 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 150d780194..934cf2a3cb 100755 --- a/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala +++ b/public/scala/qscript/org/broadinstitute/sting/queue/qscripts/GATKResourcesBundle.scala @@ -15,8 +15,8 @@ class GATKResourcesBundle extends QScript { @Argument(doc="liftOverPerl", required=false) var liftOverPerl: File = new File("./perl/liftOverVCF.pl") - @Argument(shortName = "svn", doc="The SVN version of this release", required=true) - var SVN_VERSION: String = _ + @Argument(shortName = "ver", doc="The SVN version of this release", required=true) + var 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") @@ -32,8 +32,8 @@ class GATKResourcesBundle extends QScript { val SITES_EXT: String = "sites" - def BUNDLE_DIR: File = BUNDLE_ROOT + "/" + SVN_VERSION - def DOWNLOAD_DIR: File = DOWNLOAD_ROOT + "/" + SVN_VERSION + def BUNDLE_DIR: File = BUNDLE_ROOT + "/" + VERSION + def DOWNLOAD_DIR: File = DOWNLOAD_ROOT + "/" + VERSION // REFERENCES class Reference( val name: String, val file: File ) { } @@ -113,6 +113,12 @@ class GATKResourcesBundle extends QScript { addResource(new Resource(hg19.file, "", hg19, false)) addResource(new Resource(hg18.file, "", hg18, false)) + // + // The b37_decoy reference + // + addResource(new Resource("/humgen/1kg/reference/human_g1k_v37_decoy.fasta", + "IGNORE", b37, false, false)) + // // standard VCF files. Will be lifted to each reference //