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Received permission from Mauricio to archive the DPP and PBPP PipelineTests

This commit is contained in:
Eric Banks 2013-01-07 14:03:08 -05:00
parent b4e7b3d691
commit 78f7a4e300
2 changed files with 0 additions and 113 deletions
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67
public/scala/test/org/broadinstitute/sting/queue/pipeline/DataProcessingPipelineTest.scala
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@ -1,67 +0,0 @@
package org.broadinstitute.sting.queue.pipeline
/*
* Copyright (c) 2011, The Broad Institute
*
* Permission is hereby granted, free of charge, to any person
* obtaining a copy of this software and associated documentation
* files (the "Software"), to deal in the Software without
* restriction, including without limitation the rights to use,
* copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the
* Software is furnished to do so, subject to the following
* conditions:
*
* The above copyright notice and this permission notice shall be
* included in all copies or substantial portions of the Software.
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
* OTHER DEALINGS IN THE SOFTWARE.
*/
import org.testng.annotations.Test
import org.broadinstitute.sting.BaseTest
class DataProcessingPipelineTest {
@Test(timeOut=36000000)
def testSimpleBAM {
val projectName = "test1"
val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam"
val spec = new PipelineTestSpec
spec.name = "DataProcessingPipeline"
spec.args = Array(
" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala",
" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
" -i " + BaseTest.publicTestDir + "exampleBAM.bam",
" -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf",
" -test ",
" -p " + projectName).mkString
spec.fileMD5s += testOut -> "45d97df6d291695b92668e8a55c54cd0"
PipelineTest.executeTest(spec)
}
@Test(timeOut=36000000)
def testBWAPEBAM {
val projectName = "test2"
val testOut = projectName + ".exampleBAM.bam.clean.dedup.recal.bam"
val spec = new PipelineTestSpec
spec.name = "DataProcessingPipeline"
spec.args = Array(
" -S public/scala/qscript/org/broadinstitute/sting/queue/qscripts/DataProcessingPipeline.scala",
" -R " + BaseTest.publicTestDir + "exampleFASTA.fasta",
" -i " + BaseTest.publicTestDir + "exampleBAM.bam",
" -D " + BaseTest.publicTestDir + "exampleDBSNP.vcf",
" -test ",
" -bwa /home/unix/carneiro/bin/bwa",
" -bwape ",
" -p " + projectName).mkString
spec.fileMD5s += testOut -> "9fca827ecc8436465b831bb6f879357a"
PipelineTest.executeTest(spec)
}
}

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