From 9644f104c49ed50c8894722ea971d68e274b74ca Mon Sep 17 00:00:00 2001 From: David Roazen Date: Fri, 1 Jul 2011 13:13:24 -0400 Subject: [PATCH 1/2] Fixes to the queue pipeline tests to account for the new directory structure. --- .../pipeline/examples/ExampleCountLociPipelineTest.scala | 2 +- .../queue/pipeline/examples/HelloWorldPipelineTest.scala | 6 +++--- 2 files changed, 4 insertions(+), 4 deletions(-) diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala index 2b3b51783..09f80f2c3 100644 --- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala +++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/ExampleCountLociPipelineTest.scala @@ -35,7 +35,7 @@ class ExampleCountLociPipelineTest { val spec = new PipelineTestSpec spec.name = "countloci" spec.args = Array( - " -S scala/qscript/examples/ExampleCountLoci.scala", + " -S public/scala/qscript/examples/ExampleCountLoci.scala", " -R " + BaseTest.hg18Reference, " -I " + BaseTest.validationDataLocation + "small_bam_for_countloci.bam", " -o " + testOut).mkString diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala index 8b8fa86a4..37531e791 100644 --- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala +++ b/public/scala/test/org/broadinstitute/sting/queue/pipeline/examples/HelloWorldPipelineTest.scala @@ -32,7 +32,7 @@ class HelloWorldPipelineTest { def testHelloWorld { val spec = new PipelineTestSpec spec.name = "HelloWorld" - spec.args = "-S scala/qscript/examples/HelloWorld.scala" + spec.args = "-S public/scala/qscript/examples/HelloWorld.scala" PipelineTest.executeTest(spec) } @@ -40,7 +40,7 @@ class HelloWorldPipelineTest { def testHelloWorldWithPrefix { val spec = new PipelineTestSpec spec.name = "HelloWorldWithPrefix" - spec.args = "-S scala/qscript/examples/HelloWorld.scala -jobPrefix HelloWorld" + spec.args = "-S public/scala/qscript/examples/HelloWorld.scala -jobPrefix HelloWorld" PipelineTest.executeTest(spec) } @@ -48,7 +48,7 @@ class HelloWorldPipelineTest { def testHelloWorldWithPriority { val spec = new PipelineTestSpec spec.name = "HelloWorldWithPriority" - spec.args = "-S scala/qscript/examples/HelloWorld.scala -jobPriority 100" + spec.args = "-S public/scala/qscript/examples/HelloWorld.scala -jobPriority 100" PipelineTest.executeTest(spec) } } From 11d4af0e7528d0d3dd8b5da3745ad7d7bced7280 Mon Sep 17 00:00:00 2001 From: David Roazen Date: Fri, 1 Jul 2011 13:41:34 -0400 Subject: [PATCH 2/2] Path-related fixes to the private queue pipeline tests. --- .../pipeline/IPFLibraryPipelineTest.scala | 71 ------------------- 1 file changed, 71 deletions(-) delete mode 100755 public/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryPipelineTest.scala diff --git a/public/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryPipelineTest.scala b/public/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryPipelineTest.scala deleted file mode 100755 index 6b32e5c9d..000000000 --- a/public/scala/test/org/broadinstitute/sting/queue/pipeline/IPFLibraryPipelineTest.scala +++ /dev/null @@ -1,71 +0,0 @@ -package org.broadinstitute.sting.queue.pipeline - -import org.testng.annotations.Test -import org.broadinstitute.sting.BaseTest - -class IPFLibraryPipelineTest { - - @Test - def testVCFExtractSites { - var testOut = "vcfes.vcf" - val spec = new PipelineTestSpec - spec.name = "vcfExtractSites" - spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFExtractSites -ivcf %s -out %s".format( - BaseTest.validationDataLocation + "omni_1212.subset.b37.vcf", testOut - ) - spec.fileMD5s += testOut -> "4f496b8cf90302428a9edda486a337f4" - PipelineTest.executeTest(spec) - } - - @Test - def testVCFExtractSamples { - var testOut = "vcf.extract.samples.vcf" - val spec = new PipelineTestSpec - spec.name = "vcfExtractSamples" - spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFExtractSamples -ivcf %s -out %s -sm HG00107,HG00500,NA18501,NA18942".format( - BaseTest.validationDataLocation + "omni_1212.subset.b37.vcf", testOut - ) - - spec.fileMD5s += testOut -> "180d5a2e7a1fbc5117de6705bde3a7c8" - } - - @Test - def testVCFExtractIntervals { - var testOut = "vcf.extract.intervals.list" - val spec = new PipelineTestSpec - spec.name = "vcfExtractIntervals" - spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFExtractIntervals -ivcf %s -out %s".format( - BaseTest.validationDataLocation + "omni_1212.subset.b37.vcf", testOut - ) - - spec.fileMD5s += testOut ->"28589eeb28fac753577c027abf939345" - - } - - @Test - def testVCFSimpleMerge { - var testOut = "vcf.simplemerge.vcf" - val spec = new PipelineTestSpec - val int1 = BaseTest.validationDataLocation + "omni.subset.interleaved.1.vcf" - val int2 = BaseTest.validationDataLocation + "omni.subset.interleaved.2.vcf" - spec.name = "vcfSimpleMerge" - spec.args = "-S scala/qscript/oneoffs/QTools.q -T VCFSimpleMerge -vcfs %s,%s -out %s -ref %s".format( - int1,int2,testOut,BaseTest.b37KGReference - ) - - spec.fileMD5s += testOut -> "c59b8de64ba787a2ca3a1734bdebf277" - } - - @Test - def testSortByRef { - var testOut = "vcf.refsorted.vcf" - val spec = new PipelineTestSpec - val unsorted = BaseTest.validationDataLocation + "omni.pos_sorted.vcf" - spec.name = "sortByRef" - spec.args = "-S scala/qscript/oneoffs/QTools.q -T SortByRef -ivcf %s -out %s -ref %s".format( - unsorted, testOut, BaseTest.b37KGReference - ) - - spec.fileMD5s += testOut -> "ee09af803bc94987d55d044c2ebbc0b8" - } -}