Update build.xml to make it oneoffprojects-aware, and do some misc formatting cleanup and moves.
Here goes nothing. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2234 348d0f76-0448-11de-a6fe-93d51630548a
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hanna
parent
46f3d3e39b
commit
357abc9e89
180
build.xml
180
build.xml
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@ -2,9 +2,10 @@
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<description>Compile and distribute the Sting toolkit</description>
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<property name="source.dir" value="java/src" />
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<property name="dist.dir" value="dist" />
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<property name="single" value="*Test" />
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<property name="singleintegration" value="*IntegrationTest" />
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<property name="dist" value="dist" />
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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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@ -18,20 +19,7 @@
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<!-- Set target based on STING_BUILD_TYPE environment variable -->
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<property environment="env"/>
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<condition property="target" value="playground" else="core">
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<equals arg1="${env.STING_BUILD_TYPE}" arg2="playground" casesensitive="false"/>
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</condition>
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<patternset id="dependency.mask" includes="*.jar">
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<exclude name="junit*.jar" />
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<exclude name="bcel*.jar" />
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</patternset>
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<path id="runtime.dependencies">
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<fileset dir="lib">
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<patternset refid="dependency.mask" />
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</fileset>
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</path>
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<property name="target" value="${env.STING_BUILD_TYPE}" />
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<!-- ivy properties -->
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<property name="ivy.install.version" value="2.0.0"/>
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@ -54,67 +42,76 @@
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<ivy:retrieve file="ivy.xml" conf="${ivy.conf}" />
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</target>
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<!-- where to put reports and tests-->
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<property name="report" value="build/report"/>
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<property name="test.classes" value="build/testclasses"/>
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<property name="test.output" value="${dist}/test"/>
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<property name="test.sources" value="java/test"/>
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<property name="classes" value="classes"/>
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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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<!-- Create the time stamp -->
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<tstamp/>
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<echo message="Compiling module ${target}"/>
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<!-- Create the build directory structure used by compile -->
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<mkdir dir="build"/>
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<echo message="Compiling module ${target}"/>
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<condition property="include.oneoffs">
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<equals arg1="${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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<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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<!-- Create the build directory structure used by compile -->
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<mkdir dir="build"/>
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</target>
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<target name="compile" depends="init,resolve"
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description="compile the source">
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<condition property="target.is.playground" value="true">
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<equals arg1="${target}" arg2="playground"/>
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</condition>
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<!-- Compile the java code from ${src} into build -->
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<javac srcdir="${source.dir}" destdir="build" debug="true" debuglevel="lines,vars,source" classpathref="runtime.dependencies">
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<!--compilerarg value="-Xlint:unchecked" /-->
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<exclude name="**/playground/**" unless="target.is.playground"/>
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</javac>
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<!-- Compile the java code from ${src} into build -->
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<javac srcdir="${source.dir}" destdir="build" 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="dist" depends="compile"
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description="generate the distribution">
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<mkdir dir="${dist}"/>
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<mkdir dir="${dist.dir}"/>
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<delete>
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<fileset dir="${dist}" includes="*.jar" />
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<fileset dir="${dist.dir}" includes="*.jar" />
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</delete>
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<copy todir="${dist}">
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<copy todir="${dist.dir}">
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<fileset dir="lib" includes="*.jar"/>
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</copy>
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<jar jarfile="${dist}/StingUtils.jar">
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<jar jarfile="${dist.dir}/StingUtils.jar">
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<fileset dir="build" includes="**/utils/**/*.class"/>
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</jar>
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<jar jarfile="${dist}/GenomeAnalysisTK.jar">
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<jar jarfile="${dist.dir}/GenomeAnalysisTK.jar">
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<fileset dir="build">
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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="${dist}/Aligner.jar">
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<jar jarfile="${dist.dir}/Aligner.jar">
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<fileset dir="build" includes="**/alignment/**/*.class" />
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</jar>
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<jar jarfile="${dist}/AnalyzeCovariates.jar" whenmanifestonly="skip">
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<jar jarfile="${dist.dir}/AnalyzeCovariates.jar" whenmanifestonly="skip">
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<fileset dir="build">
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<include name="**/analyzecovariates/**/*.class" />
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<include name="**/gatk/walkers/recalibration/*.class" />
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@ -134,18 +131,9 @@
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</jar>
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<jar jarfile="${dist}/Playground.jar" whenmanifestonly="skip">
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<fileset dir="build">
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<include name="**/*.class"/>
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<exclude name="**/utils/**"/>
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<exclude name="**/gatk/**"/>
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<exclude name="**/secondarybase/**" />
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</fileset>
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</jar>
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<pathconvert property="jar.classpath" pathsep=" ">
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<flattenmapper/>
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<fileset dir="${dist}" includes="*.jar"/>
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<fileset dir="${dist.dir}" includes="*.jar"/>
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<filelist files="GATKScala.jar"/>
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</pathconvert>
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@ -161,38 +149,38 @@
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</manifest>
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</jar>
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<jar jarfile="${dist}/GenomeAnalysisTK.jar" update="true">
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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="${dist}/AnalyzeCovariates.jar" update="true" whenmanifestonly="skip">
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<jar jarfile="${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}/Playground.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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<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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<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="test.compile" depends="playground">
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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="test.compile" depends="oneoffs">
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<echo message="Sting: Compiling test cases!"/>
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<mkdir dir="${test.classes}"/>
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<javac destdir="${test.classes}" debug="true" optimize="on">
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@ -222,7 +210,7 @@
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<path id="scala.classpath">
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<pathelement location="lib/scala-compiler-2.7.7.jar"/>
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<pathelement location="lib/scala-library-2.7.7.jar"/>
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<fileset dir="${dist}">
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<fileset dir="${dist.dir}">
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<patternset id="scalaStuff">
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<include name="*.jar"/>
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</patternset>
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@ -237,7 +225,7 @@
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<include name="**/*.scala"/>
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</scalac>
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<jar jarfile="${dist}/GATKScala.jar">
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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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@ -245,7 +233,11 @@
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</target>
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<!-- where to put reports and tests-->
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<property name="report" value="build/report"/>
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<property name="test.classes" value="build/testclasses"/>
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<property name="test.output" value="${dist.dir}/test"/>
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<property name="test.sources" value="java/test"/>
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<!-- TEST -->
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<target name="test" depends="test.compile,agent" description="Run unit tests">
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@ -280,7 +272,7 @@
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<formatter type="${testOutput}" usefile="${usefile}" />
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<classpath>
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<path refid="runtime.dependencies"/>
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<pathelement location="${dist}/GenomeAnalysisTK.jar"/>
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<pathelement location="${dist.dir}/GenomeAnalysisTK.jar"/>
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<pathelement location="${test.classes}"/>
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<pathelement location="lib/junit-4.4.jar"/>
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</classpath>
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@ -310,20 +302,24 @@
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</target>
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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 can't take the same dirsets as javac; it only likes getting the base directory -->
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<!-- Exclude playground files with excludepackagenames instead of the "source" dirset -->
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<condition property="package.excludes" value="" else="org.broadinstitute.sting.playground.*">
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<equals arg1="${target}" arg2="playground" />
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</condition>
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<javadoc destdir="javadoc" sourcepath="${source.dir}" excludepackagenames="${package.excludes}" classpathref="runtime.dependencies"/>
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<mkdir dir="javadoc"/>
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<javadoc destdir="javadoc"
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classpathref="runtime.dependencies">
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<fileset dir="${source.dir}">
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<patternset>
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<include name="**/*.java"/>
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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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</fileset>
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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="${dist}">
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<fileset dir="${dist.dir}">
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<patternset refid="dependency.mask" />
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</fileset>
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</unjar>
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@ -331,9 +327,9 @@
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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="${dist}/packages" />
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<xslt in="packages/${executable}.xml" out="${dist}/packages/Build${executable}.xml" style="packages/CreatePackager.xsl" />
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<ant antfile="${dist}/packages/Build${executable}.xml" />
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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" />
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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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@ -342,10 +338,10 @@
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<!-- Build out a classpath -->
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<pathconvert property="required.picard.jars" pathsep=":">
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<fileset dir="${basedir}">
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<include name="staging" />
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<include name="lib/picard-*.*.*.jar" />
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<include name="lib/sam-*.jar" />
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</fileset>
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<include name="staging" />
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<include name="lib/picard-*.*.*.jar" />
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<include name="lib/sam-*.jar" />
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</fileset>
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</pathconvert>
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<echo message="required.picard.jars=${required.picard.jars}" />
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@ -355,9 +351,9 @@
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<unjar src="${picard.dist.dir}/picard-private.jar" dest="staging" overwrite="true" />
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<!-- Use the packaging system to extract parts of picard-private we need -->
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<mkdir dir="${dist}/packages" />
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<xslt in="packages/PicardPrivate.xml" out="${dist}/packages/BuildPicardPrivate.xml" style="packages/CreatePackager.xsl" />
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<ant antfile="${dist}/packages/BuildPicardPrivate.xml">
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<mkdir dir="${dist.dir}/packages" />
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<xslt in="packages/PicardPrivate.xml" out="${dist.dir}/packages/BuildPicardPrivate.xml" style="packages/CreatePackager.xsl" />
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<ant antfile="${dist.dir}/packages/BuildPicardPrivate.xml">
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<property name="additional.jars" value="${required.picard.jars}" />
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</ant>
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</target>
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@ -367,6 +363,6 @@
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<delete dir="build"/>
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<delete dir="lib"/>
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<delete dir="staging"/>
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<delete dir="${dist}"/>
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<delete dir="${dist.dir}"/>
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</target>
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</project>
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