528 lines
22 KiB
XML
528 lines
22 KiB
XML
<project name="Sting" default="dist" basedir="." xmlns:ivy="antlib:org.apache.ivy.ant">
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<description>Compile and distribute the Sting toolkit</description>
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<property name="build.sysclasspath" value="first" />
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<property name="build.dir" value="build" />
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<property name="dist.dir" value="dist" />
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<property name="java.source.dir" value="java/src" />
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<property name="java.classes" value="${build.dir}/java/classes" />
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<property name="resource.file" value="StingText.properties" />
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<!-- where to find the tribble distro -->
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<property name="tribble.dir" value="tribble" />
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<!-- where to find 'findbugs', which you must set if you plan to use 'ant findbugs' -->
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<property name="findbugs.home" value="./findbugs"/>
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<!-- do we want to halt on failure of a junit test? default to yes (Bamboo uses 'no') -->
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<property name="halt" value="yes" />
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<!-- should our junit test output go to a file or the screen?
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false means it goes to the screen (default) true to file -->
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<property name="usefile" value="false" />
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<!-- If running the 'package' task, this property controls the name of the xml file to package -->
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<property name="executable" value="GenomeAnalysisTK" />
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<!-- Set target based on STING_BUILD_TYPE environment variable -->
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<property environment="env"/>
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<property name="target" value="${env.STING_BUILD_TYPE}" />
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<dirset id="java.source.files" dir="${java.source.dir}">
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<patternset>
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<include name="org/broadinstitute/sting/**"/>
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<exclude name="**/playground/**" unless="include.playground" />
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<exclude name="**/oneoffprojects/**" unless="include.oneoffs" />
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</patternset>
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</dirset>
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<!-- the path for resources that need to go into the GATK jar;
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any additional resources should go into this set. -->
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<path id="gatk.resources">
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<fileset dir="${java.source.dir}">
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<include name="**/**/templates/*" />
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</fileset>
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</path>
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<patternset id="dependency.mask" includes="*.jar">
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<exclude name="junit*.jar" />
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<exclude name="bcel*.jar" />
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</patternset>
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<path id="runtime.dependencies">
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<fileset dir="lib">
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<patternset refid="dependency.mask" />
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</fileset>
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</path>
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<path id="classpath">
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<path refid="runtime.dependencies" />
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<pathelement location="${java.classes}" />
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</path>
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<!-- ivy properties -->
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<property name="ivy.install.version" value="2.0.0"/>
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<property name="ivy.home" value="${user.home}/.ant"/>
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<property name="ivy.jar.dir" value="${ivy.home}/lib"/>
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<property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar"/>
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<property name="ivy.settings.dir" value="settings"/>
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<property file="${ivy.settings.dir}/ivysettings.properties"/>
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<property name="ivy.conf" value="default"/>
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<target name="resolve" depends="init"
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description="locate and download library dependencies">
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<mkdir dir="${ivy.jar.dir}"/>
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<get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
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dest="${ivy.jar.dir}/${ivy.jar.file}"
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usetimestamp="true"/>
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<taskdef resource="org/apache/ivy/ant/antlib.xml"
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uri="antlib:org.apache.ivy.ant"
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classpath="${ivy.jar.dir}/${ivy.jar.file}"/>
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<ivy:settings file="${ivy.settings.dir}/ivysettings.xml"/>
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<ivy:retrieve file="ivy.xml" conf="${ivy.conf}" />
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</target>
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<!-- define some key locations that might change based on how the build is run -->
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<target name="init">
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<!-- define build version and timestamp -->
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<exec executable="svnversion" outputproperty="build.version" failonerror="true">
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<arg value="--no-newline"/>
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</exec>
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<tstamp>
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<format property="build.timestamp" pattern="yyyy/MM/dd HH:mm:ss"/>
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</tstamp>
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<echo message="Compiling module: ${target}"/>
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<echo message="source revision : ${build.version}"/>
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<echo message="build time : ${build.timestamp}" />
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<condition property="include.oneoffs">
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<equals arg1="${target}" arg2="oneoffs" casesensitive="false" />
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</condition>
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<condition property="include.playground">
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<or>
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<equals arg1="${target}" arg2="playground" casesensitive="false"/>
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<equals arg1="${target}" arg2="oneoffs" casesensitive="false" />
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</or>
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</condition>
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<!-- Create the build directory structure used by compile -->
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<mkdir dir="${build.dir}"/>
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<mkdir dir="${java.classes}"/>
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</target>
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<target name="java.compile" depends="tribble,init,resolve"
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description="compile the source">
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<!-- Compile the java code from ${src} into build -->
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<javac srcdir="${java.source.dir}" destdir="${java.classes}" debug="true" debuglevel="lines,vars,source" classpathref="runtime.dependencies">
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<exclude name="**/playground/**" unless="include.playground"/>
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<exclude name="**/oneoffprojects/**" unless="include.oneoffs"/>
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</javac>
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</target>
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<target name="extracthelp" depends="init,java.compile"
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description="Extract help key/value pair file from the JavaDoc tags."
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unless="disable.help">
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<javadoc doclet="org.broadinstitute.sting.utils.help.ResourceBundleExtractorDoclet"
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docletpathref="classpath"
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classpathref="runtime.dependencies"
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additionalparam="-build-timestamp "${build.timestamp}" -version-suffix .${build.version} -out ${basedir}/${java.classes}/${resource.file}">
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<packageset refid="java.source.files"/>
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</javadoc>
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</target>
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<target name="dist" depends="java.compile,extracthelp"
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description="generate the distribution">
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<mkdir dir="${dist.dir}"/>
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<delete>
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<fileset dir="${dist.dir}" includes="*.jar" />
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</delete>
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<copy todir="${dist.dir}">
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<fileset dir="lib" includes="*.jar"/>
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</copy>
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<jar jarfile="${dist.dir}/StingUtils.jar">
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<fileset dir="${java.classes}" includes="**/utils/**/*.class"/>
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<manifest>
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<attribute name="Premain-Class" value="org.broadinstitute.sting.utils.instrumentation.Sizeof" />
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</manifest>
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</jar>
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<jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
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<path refid="gatk.resources"/>
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<fileset dir="${java.classes}">
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<include name="${resource.file}" />
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<include name="**/gatk/**/*.class" />
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<include name="**/alignment/**/*.class"/>
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<include name="**/oneoffprojects/**/*.class" />
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</fileset>
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<manifest>
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<attribute name="Main-Class" value="org.broadinstitute.sting.gatk.CommandLineGATK" />
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</manifest>
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</jar>
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<jar jarfile="${dist.dir}/Aligner.jar">
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<fileset dir="${java.classes}" includes="**/alignment/**/*.class" />
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</jar>
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<jar jarfile="${dist.dir}/AnalyzeCovariates.jar" whenmanifestonly="skip">
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<fileset dir="${java.classes}">
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<include name="**/analyzecovariates/**/*.class" />
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<include name="**/gatk/walkers/recalibration/*.class" />
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</fileset>
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<manifest>
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<attribute name="Main-Class" value="org.broadinstitute.sting.analyzecovariates.AnalyzeCovariates" />
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</manifest>
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</jar>
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<jar jarfile="${dist.dir}/CGUtilities.jar" whenmanifestonly="skip">
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<fileset dir="${java.classes}">
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<include name="**/*.class" />
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</fileset>
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<manifest>
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<attribute name="Main-Class" value="org.broadinstitute.sting.playground.tools.CGUtilities" />
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</manifest>
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</jar>
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<jar jarfile="${dist.dir}/VCFTool.jar" whenmanifestonly="skip">
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<fileset dir="${java.classes}">
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<include name="**/*.class"/>
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</fileset>
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<manifest>
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<attribute name="Main-Class" value="org.broadinstitute.sting.playground.tools.vcf.VCFTool" />
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</manifest>
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</jar>
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<pathconvert property="jar.classpath" pathsep=" ">
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<flattenmapper/>
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<fileset dir="${dist.dir}" includes="*.jar"/>
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<filelist files="GATKScala.jar"/>
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</pathconvert>
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<jar jarfile="${dist.dir}/VCFTool.jar" update="true" >
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<manifest>
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<attribute name="Class-Path" value="${jar.classpath}" />
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</manifest>
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</jar>
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<jar jarfile="${dist.dir}/StingUtils.jar" update="true">
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<manifest>
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<attribute name="Class-Path" value="${jar.classpath}"/>
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</manifest>
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</jar>
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<jar jarfile="${dist.dir}/GenomeAnalysisTK.jar" update="true">
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<manifest>
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<attribute name="Class-Path" value="${jar.classpath}"/>
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</manifest>
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</jar>
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<jar jarfile="${dist.dir}/AnalyzeCovariates.jar" update="true" whenmanifestonly="skip">
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<manifest>
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<attribute name="Class-Path" value="${jar.classpath}" />
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</manifest>
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</jar>
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<jar jarfile="${dist.dir}/CGUtilities.jar" update="true" whenmanifestonly="skip">
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<manifest>
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<attribute name="Class-Path" value="${jar.classpath}" />
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</manifest>
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</jar>
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</target>
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<target name="core" description="force a build of the Sting core code">
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<antcall target="dist" inheritAll="true">
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<param name="target" value="core" />
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</antcall>
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</target>
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<target name="playground" description="force a build of the Sting experimental code">
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<antcall target="dist" inheritAll="true">
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<param name="target" value="playground" />
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</antcall>
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</target>
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<target name="oneoffs" description="force a build of the Sting experimental code and one-offs">
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<antcall target="dist" inheritAll="true">
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<param name="target" value="oneoffs" />
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</antcall>
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</target>
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<target name="java.test.compile" depends="oneoffs">
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<echo message="Sting: Compiling test cases!"/>
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<mkdir dir="${java.test.classes}"/>
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<javac destdir="${java.test.classes}" debug="true" optimize="on">
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<src path="${java.test.sources}"/>
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<classpath>
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<path refid="runtime.dependencies" />
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<pathelement location="${java.classes}"/>
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<pathelement location="lib/junit-4.4.jar"/>
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</classpath>
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</javac>
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</target>
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<!-- new scala target -->
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<target name="scala" description="build the scala directory">
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<antcall target="resolve">
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<param name="ivy.conf" value="scala"/>
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</antcall>
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<antcall target="dist"/>
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<property name="scala.source.dir" value="scala/src" />
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<property name="scala.classes" value="build/scala" />
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<path id="scala.classpath">
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<fileset dir="lib">
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<include name="scala-compiler-*.jar"/>
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<include name="scala-library-*.jar"/>
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</fileset>
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<fileset dir="${dist.dir}">
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<patternset id="scalaStuff">
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<include name="*.jar"/>
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</patternset>
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</fileset>
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</path>
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<taskdef resource="scala/tools/ant/antlib.xml">
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<classpath refid="scala.classpath"/>
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</taskdef>
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<mkdir dir="${scala.classes}"/>
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<echo>Building Scala...</echo>
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<scalac srcdir="${scala.source.dir}" destdir="${scala.classes}" classpathref="scala.classpath" force="changed">
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<include name="*.scala"/>
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</scalac>
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<jar jarfile="${dist.dir}/GATKScala.jar">
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<fileset dir="${scala.classes}">
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<include name="*.class"/>
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</fileset>
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</jar>
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</target>
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<!-- Queue target -->
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<target name="queue" description="build Queue">
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<antcall target="resolve">
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<param name="ivy.conf" value="queue"/>
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</antcall>
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<!-- Call dist so jar files are picked up for manifest. -->
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<antcall target="dist" />
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<property name="queue.source.dir" value="scala/src" />
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<property name="queue.classes" value="${build.dir}/scala/classes" />
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<path id="queue.classpath">
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<path refid="runtime.dependencies" />
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<pathelement location="${java.classes}" />
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</path>
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<taskdef resource="scala/tools/ant/antlib.xml">
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<classpath refid="queue.classpath"/>
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</taskdef>
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<mkdir dir="${queue.classes}"/>
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<echo>Building Queue...</echo>
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<scalac srcdir="${queue.source.dir}" destdir="${queue.classes}" classpathref="queue.classpath">
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<include name="org/broadinstitute/sting/queue/**/*.scala"/>
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</scalac>
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<pathconvert property="queuejar.classpath" pathsep=" ">
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<flattenmapper/>
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<fileset dir="${dist.dir}" includes="*.jar"/>
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</pathconvert>
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<jar jarfile="${dist.dir}/Queue.jar">
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<fileset dir="${queue.classes}">
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<include name="org/broadinstitute/sting/queue/**/*.class"/>
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</fileset>
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<manifest>
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<attribute name="Main-Class" value="org.broadinstitute.sting.queue.QCommandLine" />
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<attribute name="Class-Path" value="${queuejar.classpath}" />
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</manifest>
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</jar>
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</target>
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<!-- ***************************************************************************** -->
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<!-- *********** Tests and associated tasks ********* -->
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<!-- ***************************************************************************** -->
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<!-- where to put reports and tests-->
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<property name="report" value="${build.dir}/report"/>
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<property name="java.test.classes" value="${java.classes}/testclasses"/>
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<property name="test.output" value="${dist.dir}/test"/>
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<property name="java.test.sources" value="java/test"/>
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<!-- provide a ceiling on the memory that unit/integration tests can consume. -->
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<property name="test.maxmemory" value="2g"/>
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<!-- TEST -->
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<macrodef name="run-test">
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<attribute name="testtype"/>
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<sequential>
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<mkdir dir="${report}"/>
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<echo message="Sting: Running @{testtype} test cases!"/>
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<junit printsummary="yes" showoutput="yes" maxmemory="${test.maxmemory}" clonevm="yes" haltonfailure="${halt}" failureProperty="test.failure">
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<formatter type="brief" usefile="false" />
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<formatter type="xml"/>
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<jvmarg value="-Xdebug"/>
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<jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8091"/>
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<classpath>
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<pathelement location="${java.classes}"/>
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<path refid="runtime.dependencies"/>
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<pathelement location="${java.test.classes}"/>
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<pathelement location="lib/junit-4.4.jar"/>
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</classpath>
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<batchtest fork="yes" todir="${report}">
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<fileset dir="${java.test.classes}">
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<include name="**/@{testtype}.class"/>
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<exclude name="**/BaseTest.class"/>
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</fileset>
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</batchtest>
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</junit>
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<fail message="test failed" if="test.failure" />
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</sequential>
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</macrodef>
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<!-- our three different test conditions: Test, IntegrationTest, PerformanceTest -->
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<target name="test" depends="java.test.compile,tribble.test" description="Run unit tests">
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<condition property="ttype" value="*UnitTest" else="${single}">
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<not><isset property="single"/></not>
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</condition>
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<run-test testtype="${ttype}"/>
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</target>
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<target name="integrationtest" depends="java.test.compile" description="Run integration tests">
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<condition property="itype" value="*IntegrationTest" else="${single}">
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<not><isset property="single"/></not>
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</condition>
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<run-test testtype="${itype}"/>
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</target>
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<target name="performancetest" depends="java.test.compile" description="Run performance tests">
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<condition property="ptype" value="*PerformanceTest" else="${single}">
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<not><isset property="single"/></not>
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</condition>
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<run-test testtype="${ptype}"/>
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</target>
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<!-- ***************************************************************************** -->
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<!-- *********** Tribble ********* -->
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<!-- ***************************************************************************** -->
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<!-- compile the library -->
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<target name="tribble.compile" description="compiles the tribble library">
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<echo message="Building the Tribble Library..."/>
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<ant antfile="build.xml" target="all" dir="${tribble.dir}" inheritAll="false"/>
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</target>
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<!-- build the jar -->
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<target name="tribble" description="Builds the tribble jar" depends="tribble.compile">
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<copy todir="lib">
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<fileset dir="${tribble.dir}/dist" includes="*.jar"/>
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</copy>
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</target>
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<!-- test tribble using the unit tests set in tribble -->
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<target name="tribble.test" description="runs the tribble tests" depends="tribble.compile">
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<echo message="Testing the Tribble Library..."/>
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<ant antfile="build.xml" target="test" dir="${tribble.dir}" inheritAll="false"/>
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</target>
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<!-- clean tribble -->
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<target name="tribble.clean" description="cleans the tribble library">
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<echo message="Cleaning the Tribble Library..."/>
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<ant antfile="build.xml" target="clean" dir="${tribble.dir}" inheritAll="false"/>
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</target>
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<!-- ***************************************************************************** -->
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<target name="javadoc" depends="init,resolve" description="generates javadoc">
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<mkdir dir="javadoc"/>
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<javadoc destdir="javadoc"
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classpathref="runtime.dependencies">
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<packageset refid="java.source.files"/>
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</javadoc>
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</target>
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<!-- Unzip all classes from their current locations and assemble them in a staging directory -->
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<target name="stage" description="stage files for distribution">
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<mkdir dir="staging"/>
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<unjar dest="staging" overwrite="false">
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<fileset dir="${dist.dir}">
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<patternset refid="dependency.mask" />
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</fileset>
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</unjar>
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</target>
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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="${dist.dir}/packages" />
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<xslt in="packages/${executable}.xml" out="${dist.dir}/packages/Build${executable}.xml" style="packages/CreatePackager.xsl" />
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<ant antfile="${dist.dir}/packages/Build${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="${dist.dir}/packages/Build${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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<!-- TODO: Reuse as much as possible of the 'stage' and 'package' targets -->
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<target name="build-picard-private" depends="resolve">
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<!-- Build out a classpath -->
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|
<pathconvert property="required.picard.jars" pathsep=":">
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|
<fileset dir="${basedir}">
|
|
<include name="staging" />
|
|
<include name="lib/picard-*.*.*.jar" />
|
|
<include name="lib/sam-*.jar" />
|
|
</fileset>
|
|
</pathconvert>
|
|
<echo message="required.picard.jars=${required.picard.jars}" />
|
|
|
|
<!-- Stage picard-private -->
|
|
<delete dir="staging" />
|
|
<mkdir dir="staging" />
|
|
<unjar src="${picard.dist.dir}/picard-private.jar" dest="staging" overwrite="true" />
|
|
|
|
<!-- Use the packaging system to extract parts of picard-private we need -->
|
|
<mkdir dir="${dist.dir}/packages" />
|
|
<xslt in="packages/PicardPrivate.xml" out="${dist.dir}/packages/BuildPicardPrivate.xml" style="packages/CreatePackager.xsl" />
|
|
<ant antfile="${dist.dir}/packages/BuildPicardPrivate.xml">
|
|
<property name="additional.jars" value="${required.picard.jars}" />
|
|
</ant>
|
|
</target>
|
|
|
|
<!-- ******************************************************************************** -->
|
|
<!-- Find bug tasks -->
|
|
<!-- ******************************************************************************** -->
|
|
<path id="findbugs.classpath">
|
|
<fileset dir="lib" erroronmissingdir="true" includes="*.jar"/>
|
|
</path>
|
|
<target name="findbugs" depends="dist">
|
|
<antcall target ="resolve">
|
|
<param name ="ivy.conf" value="findbugs"/>
|
|
</antcall>
|
|
<!-- setup the taskdef, telling ant where to find the defined task for ant -->
|
|
<taskdef name="findbugs" classname="edu.umd.cs.findbugs.anttask.FindBugsTask" classpathref="findbugs.classpath"/>
|
|
<!-- what should findbug look at: we want to aim it at the GATK.jar -->
|
|
<findbugs home="${findbugs.home}"
|
|
output="xml"
|
|
outputFile="${build.dir}/findbugs.xml"
|
|
classpathref="findbugs.classpath"
|
|
debug="false">
|
|
<auxClasspath>
|
|
<fileset dir="dist" includes="**/*.jar" excludes="**/GenomeAnalysisTK.jar"/>
|
|
</auxClasspath>
|
|
<sourcePath path="../java/src" />
|
|
<class location="dist/GenomeAnalysisTK.jar" />
|
|
</findbugs>
|
|
</target>
|
|
|
|
|
|
|
|
<target name="clean" description="clean up" depends="tribble.clean">
|
|
<delete dir="out"/>
|
|
<delete dir="${build.dir}"/>
|
|
<delete dir="lib"/>
|
|
<delete dir="staging"/>
|
|
<delete dir="${dist.dir}"/>
|
|
<!-- When we clean, make sure to clean out tribble as well -->
|
|
<ant antfile="tribble/build.xml" target="clean"/>
|
|
|
|
</target>
|
|
</project>
|