Merged bug fix from Stable into Unstable
This commit is contained in:
David Roazen
commit
aad99563be
156
build.xml
156
build.xml
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@ -67,6 +67,8 @@
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<!-- If running the 'package' task, this property controls the name of the xml file to package -->
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<property name="package.xml.dir" value="${public.dir}/packages" />
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<property name="package.output.dir" value="${dist.dir}/packages" />
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<property name="staging.dir" value="staging" />
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<property name="executable" value="GenomeAnalysisTK" />
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<property environment="env"/>
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@ -118,6 +120,16 @@
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</fileset>
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</path>
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<path id="testng.dependencies">
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<fileset dir="${lib.dir}">
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<include name="jcommander*.jar"/>
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<include name="guice*.jar"/>
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<include name="junit*.jar"/>
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<include name="bsh*.jar"/>
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<include name="snakeyaml*.jar"/>
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</fileset>
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</path>
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<path id="build.results">
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<fileset dir="dist">
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<patternset refid="dependency.mask" />
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@ -829,10 +841,54 @@
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<target name="test.compile" depends="init.usecontracts,test.java.compile,test.scala.compile" />
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<path id="testng.default.classpath">
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<path refid="external.dependencies" />
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<pathelement location="${java.classes}" />
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<pathelement location="${scala.classes}" />
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<pathelement location="${java.contracts}" />
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<pathelement location="${java.public.test.classes}" />
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<pathelement location="${java.private.test.classes}" />
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<pathelement location="${scala.public.test.classes}" />
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<pathelement location="${scala.private.test.classes}" />
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</path>
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<path id="testng.gatk.releasetest.classpath">
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<path refid="testng.dependencies" />
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<path>
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<fileset dir="${package.output.dir}">
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<include name="**/${executable}.jar" />
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</fileset>
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</path>
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<pathelement location="${java.contracts}" />
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<pathelement location="${java.public.test.classes}" />
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<pathelement location="${scala.public.test.classes}" />
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<pathelement location="${scala.classes}" />
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<path>
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<fileset dir="${lib.dir}">
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<include name="scala*.jar"/>
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<include name="jna*.jar"/>
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</fileset>
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</path>
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</path>
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<path id="testng.queue.releasetest.classpath">
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<path refid="testng.dependencies" />
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<path>
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<fileset dir="${package.output.dir}">
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<include name="**/${executable}.jar" />
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</fileset>
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</path>
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<pathelement location="${java.contracts}" />
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<pathelement location="${java.public.test.classes}" />
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<pathelement location="${scala.public.test.classes}" />
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</path>
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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="classpath"/>
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<attribute name="runfailed"/>
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<sequential>
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@ -853,6 +909,7 @@
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<echo message="Sting: Running @{testtype} test cases!"/>
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<taskdef resource="testngtasks" classpath="${testng.jar}"/>
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<testng outputDir="@{outputdir}"
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classpathref="@{classpath}"
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haltOnFailure="false" failureProperty="test.failure"
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verbose="2"
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workingDir="${basedir}"
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@ -865,16 +922,6 @@
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<jvmarg line="${cofoja.jvm.args}"/>
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<!-- <jvmarg value="-Xdebug"/> -->
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<!-- <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=y,address=5005"/> -->
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<classpath>
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<path refid="external.dependencies" />
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<pathelement location="${java.classes}" />
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<pathelement location="${scala.classes}" />
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<pathelement location="${java.contracts}" />
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<pathelement location="${java.public.test.classes}" />
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<pathelement location="${java.private.test.classes}" />
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<pathelement location="${scala.public.test.classes}" />
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<pathelement location="${scala.private.test.classes}" />
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</classpath>
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<classfileset dir="${java.public.test.classes}" includes="**/@{testtype}.class"/>
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<classfileset dir="${java.private.test.classes}" erroronmissingdir="false">
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@ -904,6 +951,10 @@
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</sequential>
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</macrodef>
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<target name="test.init">
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<property name="testng.classpath" value="testng.default.classpath" />
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</target>
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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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@ -916,62 +967,81 @@
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<antcall target="pipelinetest.public" inheritAll="false"/>
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</target>
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<target name="alltests.gatk.packagejar" depends="init.buildpublic,package">
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<antcall target="test.public" inheritAll="false">
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<param name="testng.classpath" value="testng.gatk.releasetest.classpath" />
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</antcall>
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<antcall target="integrationtest.public" inheritAll="false">
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<param name="testng.classpath" value="testng.gatk.releasetest.classpath" />
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</antcall>
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</target>
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<target name="alltests.queue.packagejar" depends="init.buildpublic,queue">
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<antcall target="package" inheritAll="false">
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<param name="executable" value="Queue" />
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</antcall>
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<antcall target="pipelinetest.public" inheritAll="false">
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<param name="executable" value="Queue" />
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<param name="testng.classpath" value="testng.queue.releasetest.classpath" />
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</antcall>
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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,vcf.jar" description="Run unit tests">
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<target name="test" depends="init.buildall,test.compile,vcf.jar,test.init" 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}" outputdir="${report}/${ttype}" runfailed="false"/>
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<run-test testtype="${ttype}" outputdir="${report}/${ttype}" classpath="${testng.classpath}" runfailed="false"/>
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</target>
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<target name="test.public" depends="init.buildpublic,test"/>
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<target name="integrationtest" depends="init.buildall,test.compile" description="Run integration tests">
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<target name="integrationtest" depends="init.buildall,test.compile,test.init" description="Run integration tests">
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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}" outputdir="${report}/${itype}" runfailed="false"/>
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<run-test testtype="${itype}" outputdir="${report}/${itype}" classpath="${testng.classpath}" runfailed="false"/>
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</target>
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<target name="integrationtest.public" depends="init.buildpublic,integrationtest"/>
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<target name="performancetest" depends="init.buildall,test.compile" description="Run performance tests">
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<target name="performancetest" depends="init.buildall,test.compile,test.init" description="Run performance tests">
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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}" outputdir="${report}/${ptype}" runfailed="false"/>
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<run-test testtype="${ptype}" outputdir="${report}/${ptype}" classpath="${testng.classpath}" runfailed="false"/>
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</target>
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<target name="performancetest.public" depends="init.buildpublic,performancetest" />
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<target name="pipelinetest" depends="init.buildall,test.compile" description="Run pipeline tests">
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<target name="pipelinetest" depends="init.buildall,test.compile,test.init" description="Run pipeline tests">
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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}" outputdir="${report}/${pipetype}" runfailed="false"/>
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<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" classpath="${testng.classpath}" runfailed="false"/>
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</target>
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<target name="pipelinetest.public" depends="init.buildpublic,pipelinetest" />
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<target name="pipelinetestrun" depends="init.buildall,test.compile" description="Run pipeline tests">
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<target name="pipelinetestrun" depends="init.buildall,test.compile,test.init" description="Run pipeline tests">
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<property name="pipeline.run" value="run"/>
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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}" outputdir="${report}/${pipetype}" runfailed="false"/>
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<run-test testtype="${pipetype}" outputdir="${report}/${pipetype}" classpath="${testng.classpath}" 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="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
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<target name="failed-test" depends="init.buildall,test.compile,test.init">
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<run-test testtype="${report}/*UnitTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
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</target>
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<target name="failed-integration" depends="init.buildall,test.compile">
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<run-test testtype="${report}/*IntegrationTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
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<target name="failed-integration" depends="init.buildall,test.compile,test.init">
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<run-test testtype="${report}/*IntegrationTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" 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="${report}/*PerformanceTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
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<target name="failed-performance" depends="init.buildall,test.compile,test.init">
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<run-test testtype="${report}/*PerformanceTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
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</target>
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<target name="failed-pipeline" depends="init.buildall,test.compile">
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<run-test testtype="${report}/*PipelineTest/testng-failed.xml" outputdir="${report}/failed_rerun" runfailed="true"/>
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<target name="failed-pipeline" depends="init.buildall,test.compile,test.init">
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<run-test testtype="${report}/*PipelineTest/testng-failed.xml" outputdir="${report}/failed_rerun" classpath="${testng.classpath}" runfailed="true"/>
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</target>
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<!-- ******************************************************************************** -->
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@ -1029,14 +1099,14 @@
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<!-- Unzip all classes from their current locations and assemble them in a staging directory -->
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<target name="stage" description="stage files for distribution">
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<mkdir dir="staging"/>
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<mkdir dir="${staging.dir}"/>
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<!--
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HACK: Create the edu directory before EDU on case-insensitive mac filesystems.
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The ivy dependency colt -> concurrent contains an EDU.oswego package which
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BCEL doesn't even pull in but messes up edu.mit.broad.
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-->
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<mkdir dir="staging/edu"/>
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<unjar dest="staging" overwrite="false">
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<mkdir dir="${staging.dir}/edu"/>
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<unjar dest="${staging.dir}" overwrite="false">
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<fileset dir="${dist.dir}">
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<patternset refid="dependency.mask" />
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</fileset>
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@ -1045,8 +1115,8 @@
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<!-- Build a package consisting of all supporting files -->
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<target name="package" depends="dist,stage" description="bundle up an executable for distribution">
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<mkdir dir="dist/packages" />
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<xslt destdir="dist/packages" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false">
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<mkdir dir="${package.output.dir}" />
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<xslt destdir="${package.output.dir}" style="${package.xml.dir}/CreatePackager.xsl" useImplicitFileset="false">
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<flattenmapper/>
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<fileset dir="${package.xml.dir}">
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<include name="${executable}.xml" />
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@ -1057,11 +1127,11 @@
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</fileset>
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</xslt>
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<ant antfile="${dist.dir}/packages/${executable}.xml" target="package" />
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<ant antfile="${package.output.dir}/${executable}.xml" target="package" />
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</target>
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<target name="release" depends="package" description="release a build, putting each file in a location specified by the package">
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<ant antfile="${dist.dir}/packages/${executable}.xml" target="release" />
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<ant antfile="${package.output.dir}/${executable}.xml" target="release" />
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</target>
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<!-- Build a subset of picard with only those classes we need by completely abusing the packaging system -->
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@ -1070,7 +1140,7 @@
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<!-- Build out a classpath -->
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<pathconvert property="required.picard.jars" pathsep=":">
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<fileset dir="${basedir}">
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<include name="staging" />
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<include name="${staging.dir}" />
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<include name="${lib.dir}/picard-*.*.*.jar" />
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<include name="${lib.dir}/sam-*.jar" />
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</fileset>
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@ -1078,14 +1148,14 @@
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<echo message="required.picard.jars=${required.picard.jars}" />
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<!-- Stage picard-private -->
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<delete dir="staging" />
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<mkdir dir="staging" />
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<unjar src="${picard.dist.dir}/picard-private.jar" dest="staging" overwrite="true" />
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<delete dir="${staging.dir}" />
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<mkdir dir="${staging.dir}" />
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<unjar src="${picard.dist.dir}/picard-private.jar" dest="${staging.dir}" overwrite="true" />
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<!-- Use the packaging system to extract parts of picard-private we need -->
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<mkdir dir="${dist.dir}/packages" />
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<xslt in="${package.xml.dir}/PicardPrivate.xml" out="${dist.dir}/packages/BuildPicardPrivate.xml" style="${package.xml.dir}/CreatePackager.xsl" />
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<ant antfile="${dist.dir}/packages/BuildPicardPrivate.xml">
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<mkdir dir="${package.output.dir}" />
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<xslt in="${package.xml.dir}/PicardPrivate.xml" out="${package.output.dir}/BuildPicardPrivate.xml" style="${package.xml.dir}/CreatePackager.xsl" />
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<ant antfile="${package.output.dir}/BuildPicardPrivate.xml">
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<property name="additional.jars" value="${required.picard.jars}" />
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</ant>
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</target>
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@ -1121,7 +1191,7 @@
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<delete dir="${build.dir}"/>
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<delete dir="${lib.dir}"/>
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<delete dir="dump"/>
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<delete dir="staging"/>
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<delete dir="${staging.dir}"/>
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<delete dir="${dist.dir}"/>
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<delete dir="pipelinetests"/>
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</target>
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@ -26,14 +26,10 @@
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<package name="GATKEngine">
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<executable name="GATKEngine">
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<dependencies>
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<!-- Core walkers -->
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<package name="org.broadinstitute.sting.gatk.walkers.**" />
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<!-- All non-oneoff GATK-specific RODs -->
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<package name="org.broadinstitute.sting.utils.codecs.**" />
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<!-- Filters -->
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<package name="org.broadinstitute.sting.gatk.filters" />
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<!-- Package everything in org.broadinstitute.sting -->
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<package name="org.broadinstitute.sting.**" />
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<!-- Tribble codecs -->
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<package name="org.broad.tribble.*" />
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<package name="org.broad.tribble.**" />
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<!-- Workaround - depend on the logger impl required by JEXL -->
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<package name="org.apache.commons.logging.impl" />
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</dependencies>
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Reference in New Issue