Received permission from Mauricio to archive the DPP and PBPP PipelineTests
This commit is contained in:
Eric Banks
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package org.broadinstitute.sting.queue.pipeline
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/*
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* Copyright (c) 2011, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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import org.testng.annotations.Test
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import org.broadinstitute.sting.BaseTest
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class DataProcessingPipelineTest {
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@Test(timeOut=36000000)
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def testSimpleBAM {
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val projectName = "test1"
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val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam"
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val spec = new PipelineTestSpec
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spec.name = "DataProcessingPipeline"
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spec.args = Array(
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" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala",
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" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
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" -i " + BaseTest.publicTestDir + "exampleBAM.bam",
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" -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf",
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" -test ",
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" -p " + projectName).mkString
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spec.fileMD5s += testOut -> "45d97df6d291695b92668e8a55c54cd0"
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PipelineTest.executeTest(spec)
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}
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@Test(timeOut=36000000)
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def testBWAPEBAM {
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val projectName = "test2"
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val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam"
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val spec = new PipelineTestSpec
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spec.name = "DataProcessingPipeline"
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spec.args = Array(
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" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala",
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" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
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" -i " + BaseTest.publicTestDir + "exampleBAM.bam",
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" -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf",
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" -test ",
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" -bwa /home/unix/carneiro/bin/bwa",
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" -bwape ",
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" -p " + projectName).mkString
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spec.fileMD5s += testOut -> "9fca827ecc8436465b831bb6f879357a"
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PipelineTest.executeTest(spec)
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}
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}
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@ -1,46 +0,0 @@
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package org.broadinstitute.sting.queue.pipeline
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/*
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* Copyright (c) 2011, The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
|
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* obtaining a copy of this software and associated documentation
|
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* files (the "Software"), to deal in the Software without
|
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* restriction, including without limitation the rights to use,
|
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
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* copies of the Software, and to permit persons to whom the
|
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* Software is furnished to do so, subject to the following
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* conditions:
|
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
|
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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import org.testng.annotations.Test
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import org.broadinstitute.sting.BaseTest
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class PacbioProcessingPipelineTest {
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@Test(timeOut=36000000)
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def testPacbioProcessingPipeline {
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val testOut = "exampleBAM.recal.bam"
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val spec = new PipelineTestSpec
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spec.name = "pacbioProcessingPipeline"
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spec.args = Array(
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" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/PacbioProcessingPipeline.scala",
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" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
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" -i " + BaseTest.publicTestDir + "exampleBAM.bam",
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" -blasr ",
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" -test ",
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" -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf").mkString
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spec.fileMD5s += testOut -> "b84f9c45e045685067ded681d5e6224c"
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PipelineTest.executeTest(spec)
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}
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}
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