Merge branch 'master' of ssh://nickel.broadinstitute.org/humgen/gsa-scr1/gsa-engineering/git/unstable
This commit is contained in:
Ryan Poplin
commit
9ada9b3ed4
45
build.xml
45
build.xml
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@ -821,6 +821,7 @@
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<!-- TEST -->
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<macrodef name="run-test">
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<attribute name="testtype"/>
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<attribute name="outputdir"/>
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<attribute name="runfailed"/>
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<sequential>
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@ -828,10 +829,6 @@
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<equals arg1="@{runfailed}" arg2="true"/>
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</condition>
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<condition property="test.output.dir" value="${report}/@{testtype}" else="${report}/failed_rerun">
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<not><isset property="run.failed.tests"/></not>
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</condition>
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<!-- Get the pipeline run type. Default to dry. -->
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<condition property="pipeline.run" value="dry" else="${pipeline.run}">
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<equals arg1="${pipeline.run}" arg2="$${pipeline.run}" />
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@ -841,10 +838,10 @@
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<isset property="include.contracts" />
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</condition>
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<mkdir dir="${test.output.dir}"/>
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<mkdir dir="@{outputdir}"/>
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<echo message="Sting: Running @{testtype} test cases!"/>
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<taskdef resource="testngtasks" classpath="${testng.jar}"/>
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<testng outputDir="${test.output.dir}"
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<testng outputDir="@{outputdir}"
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haltOnFailure="false" failureProperty="test.failure"
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verbose="2"
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workingDir="${basedir}"
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@ -885,23 +882,35 @@
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</testng>
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<!-- generate a report for Bamboo or Hudson to read in -->
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<junitreport todir="${test.output.dir}">
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<fileset dir="${test.output.dir}">
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<junitreport todir="@{outputdir}">
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<fileset dir="@{outputdir}">
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<include name="*/*.xml"/>
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</fileset>
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<report format="noframes" todir="${test.output.dir}"/>
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<report format="noframes" todir="@{outputdir}"/>
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</junitreport>
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<fail message="test failed" if="test.failure" />
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</sequential>
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</macrodef>
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<target name="alltests">
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<antcall target="test" inheritAll="false"/>
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<antcall target="integrationtest" inheritAll="false"/>
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<antcall target="pipelinetest" inheritAll="false"/>
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</target>
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<target name="alltests.public">
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<antcall target="test.public" inheritAll="false"/>
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<antcall target="integrationtest.public" inheritAll="false"/>
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<antcall target="pipelinetest.public" inheritAll="false"/>
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</target>
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<!-- Our four different test conditions: Test, IntegrationTest, PerformanceTest, PipelineTest -->
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<target name="test" depends="init.buildall,test.compile" description="Run unit tests">
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<condition property="ttype" value="*UnitTest" else="${single}">
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<not><isset property="single"/></not>
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</condition>
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<run-test testtype="${ttype}" runfailed="false"/>
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<run-test testtype="${ttype}" outputdir="${report}/${ttype}" runfailed="false"/>
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</target>
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<target name="test.public" depends="init.buildpublic,test"/>
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@ -909,7 +918,7 @@
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<condition property="itype" value="*IntegrationTest" else="${single}">
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<not><isset property="single"/></not>
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</condition>
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<run-test testtype="${itype}" runfailed="false"/>
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<run-test testtype="${itype}" outputdir="${report}/${itype}" runfailed="false"/>
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</target>
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<target name="integrationtest.public" depends="init.buildpublic,integrationtest"/>
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@ -917,7 +926,7 @@
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<condition property="ptype" value="*PerformanceTest" else="${single}">
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<not><isset property="single"/></not>
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</condition>
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<run-test testtype="${ptype}" runfailed="false"/>
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<run-test testtype="${ptype}" outputdir="${report}/${ptype}" runfailed="false"/>
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</target>
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<target name="performancetest.public" depends="init.buildpublic,performancetest" />
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@ -925,7 +934,7 @@
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<condition property="pipetype" value="*PipelineTest" else="${single}">
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<not><isset property="single"/></not>
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</condition>
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<run-test testtype="${pipetype}" runfailed="false"/>
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<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/>
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</target>
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<target name="pipelinetest.public" depends="init.buildpublic,pipelinetest" />
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@ -934,24 +943,24 @@
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<condition property="pipetype" value="*PipelineTest" else="${single}">
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<not><isset property="single"/></not>
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</condition>
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<run-test testtype="${pipetype}" runfailed="false"/>
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<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" runfailed="false"/>
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</target>
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<target name="pipelinetestrun.public" depends="init.buildpublic,pipelinetestrun" />
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<target name="failed-test" depends="init.buildall,test.compile">
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<run-test testtype="${report}/*UnitTest/testng-failed.xml" runfailed="true"/>
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<run-test testtype="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
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</target>
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<target name="failed-integration" depends="init.buildall,test.compile">
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<run-test testtype="${report}/*IntegrationTest/testng-failed.xml" runfailed="true"/>
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<run-test testtype="${report}/*IntegrationTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
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</target>
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<target name="failed-performance" depends="init.buildall,test.compile">
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<run-test testtype="${report}/*PerformanceTest/testng-failed.xml" runfailed="true"/>
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<run-test testtype="${report}/*PerformanceTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
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</target>
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<target name="failed-pipeline" depends="init.buildall,test.compile">
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<run-test testtype="${report}/*PipelineTest/testng-failed.xml" runfailed="true"/>
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<run-test testtype="${report}/*PipelineTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
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</target>
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<!-- ******************************************************************************** -->
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@ -256,7 +256,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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" --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
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" --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
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WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
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1, Arrays.asList("2df4f8911ffc3c8d042298723ed465f8"));
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1, Arrays.asList("f70997b6a3e7fdc89d11e1d61a2463d4"));
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executeTestParallel("testSelect1", spec);
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}
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@ -273,7 +273,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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@Test
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public void testCompVsEvalAC() {
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String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ed54aa127b173d8ad8b6482f2a929a42"));
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("407682de41dcf139ea635e9cda21b912"));
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executeTestParallel("testCompVsEvalAC",spec);
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}
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@ -303,7 +303,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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" --dbsnp " + b37dbSNP132 +
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" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
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" -noST -ST Novelty -o %s";
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("18c44636e36d6657110bf984f8eac181"));
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("424c9d438b1faa59b2c29413ba32f37b"));
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executeTestParallel("testEvalTrackWithoutGenotypes",spec);
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}
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@ -315,7 +315,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
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" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
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" --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
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" -noST -ST Novelty -o %s";
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("1b8ae4fd10de0888bd843f833859d990"));
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WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("18fa0b89ebfff51141975d7e4ce7a159"));
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executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
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}
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@ -98,7 +98,7 @@ public class VCFStreamingIntegrationTest extends WalkerTest {
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" -EV CompOverlap -noEV -noST" +
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" -o %s",
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1,
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Arrays.asList("ea09bf764adba9765b99921c5ba2c709")
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Arrays.asList("d46a735ffa898f4aa6b3758c5b03f06d")
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);
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executeTest("testVCFStreamingChain", selectTestSpec);
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