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build.xml
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build.xml
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<?xml version="1.0" encoding="UTF-8"?>
<project name="out" default="all">
<property file="build.properties"/>
<!-- Uncomment the following property if no tests compilation is needed -->
<!--
<property name="skip.tests" value="true"/>
-->
<!-- Compiler options -->
<property name="compiler.debug" value="on"/>
<property name="compiler.generate.no.warnings" value="off"/>
<property name="compiler.args" value=""/>
<property name="compiler.max.memory" value="256m"/>
<patternset id="ignored.files">
<exclude name="**/CVS/**"/>
<exclude name="**/SCCS/**"/>
<exclude name="**/RCS/**"/>
<exclude name="**/rcs/**"/>
<exclude name="**/.DS_Store/**"/>
<exclude name="**/.svn/**"/>
<exclude name="**/.pyc/**"/>
<exclude name="**/.pyo/**"/>
<exclude name="**/*.pyc/**"/>
<exclude name="**/*.pyo/**"/>
<exclude name="**/.git/**"/>
<exclude name="**/*.hprof/**"/>
<exclude name="**/_svn/**"/>
<exclude name="**/.hg/**"/>
<exclude name="**/*.lib/**"/>
<exclude name="**/*~/**"/>
<exclude name="**/__pycache__/**"/>
<exclude name="**/.bundle/**"/>
<exclude name="**/*.rbc/**"/>
</patternset>
<patternset id="compiler.excluded"/>
<patternset id="library.patterns">
<include name="*.zip"/>
<include name="*.apk"/>
<include name="*.war"/>
<include name="*.egg"/>
<include name="*.ear"/>
<include name="*.ane"/>
<include name="*.swc"/>
<include name="*.jar"/>
</patternset>
<patternset id="compiler.resources">
<include name="**/?*.properties"/>
<include name="**/?*.xml"/>
<include name="**/?*.gif"/>
<include name="**/?*.png"/>
<include name="**/?*.jpeg"/>
<include name="**/?*.jpg"/>
<include name="**/?*.html"/>
<include name="**/?*.dtd"/>
<include name="**/?*.tld"/>
<include name="**/?*.ftl"/>
</patternset>
<!-- Project Libraries -->
<path id="library.commons_math.classpath">
<pathelement location="${basedir}/lib/commons-math3-3.2.jar"/>
</path>
<path id="library.genomeanalysistk.classpath">
<fileset dir="${basedir}/lib/GenomeAnalysisTK-1.5-32-g2761da9">
<patternset refid="library.patterns"/>
</fileset>
</path>
<path id="library.jsc.classpath">
<pathelement location="${basedir}/lib/jsc.jar"/>
</path>
<!-- Modules -->
<!-- Module Seurat -->
<dirname property="module.seurat.basedir" file="${ant.file}"/>
<property name="compiler.args.seurat" value="${compiler.args}"/>
<property name="seurat.output.dir" value="${module.seurat.basedir}/out/production/Seurat"/>
<property name="seurat.testoutput.dir" value="${module.seurat.basedir}/out/test/Seurat"/>
<path id="seurat.module.bootclasspath">
<!-- Paths to be included in compilation bootclasspath -->
</path>
<path id="seurat.module.production.classpath">
<path refid="library.jsc.classpath"/>
<path refid="library.commons_math.classpath"/>
<path refid="library.genomeanalysistk.classpath"/>
</path>
<path id="seurat.runtime.production.module.classpath">
<pathelement location="${seurat.output.dir}"/>
<path refid="library.jsc.classpath"/>
<path refid="library.commons_math.classpath"/>
<path refid="library.genomeanalysistk.classpath"/>
</path>
<path id="seurat.module.classpath">
<pathelement location="${seurat.output.dir}"/>
<path refid="library.jsc.classpath"/>
<path refid="library.commons_math.classpath"/>
<path refid="library.genomeanalysistk.classpath"/>
</path>
<path id="seurat.runtime.module.classpath">
<pathelement location="${seurat.testoutput.dir}"/>
<pathelement location="${seurat.output.dir}"/>
<path refid="library.jsc.classpath"/>
<path refid="library.commons_math.classpath"/>
<path refid="library.genomeanalysistk.classpath"/>
</path>
<patternset id="excluded.from.module.seurat">
<patternset refid="ignored.files"/>
</patternset>
<patternset id="excluded.from.compilation.seurat">
<patternset refid="compiler.excluded"/>
<patternset refid="excluded.from.module.seurat"/>
</patternset>
<path id="seurat.module.sourcepath">
<dirset dir="${module.seurat.basedir}/Seurat">
<include name="src"/>
</dirset>
</path>
<target name="compile.module.seurat" depends="compile.module.seurat.production,compile.module.seurat.tests" description="Compile module Seurat"/>
<target name="compile.module.seurat.production" description="Compile module Seurat; production classes">
<mkdir dir="${seurat.output.dir}"/>
<javac destdir="${seurat.output.dir}" debug="${compiler.debug}" nowarn="${compiler.generate.no.warnings}" memorymaximumsize="${compiler.max.memory}" fork="true">
<compilerarg line="${compiler.args.seurat}"/>
<bootclasspath refid="seurat.module.bootclasspath"/>
<classpath refid="seurat.module.production.classpath"/>
<src refid="seurat.module.sourcepath"/>
<patternset refid="excluded.from.compilation.seurat"/>
</javac>
<copy todir="${seurat.output.dir}/org/broadinstitute/sting/gatk/walkers/tgen">
<fileset dir="${module.seurat.basedir}/Seurat/src">
<patternset refid="compiler.resources"/>
<type type="file"/>
<patternset refid="excluded.from.compilation.seurat"/>
</fileset>
</copy>
</target>
<target name="compile.module.seurat.tests" depends="compile.module.seurat.production" description="compile module Seurat; test classes" unless="skip.tests"/>
<target name="clean.module.seurat" description="cleanup module">
<delete dir="${seurat.output.dir}"/>
<delete dir="${seurat.testoutput.dir}"/>
</target>
<target name="init" description="Build initialization">
<!-- Perform any build initialization in this target -->
</target>
<target name="clean" depends="clean.module.seurat" description="cleanup all"/>
<target name="build.modules" depends="init, clean, compile.module.seurat" description="build all modules"/>
<target name="init.artifacts">
<property name="artifacts.temp.dir" value="${basedir}/__artifacts_temp"/>
<property name="artifact.output.seurat:jar" value="${basedir}/out/artifacts/Seurat_jar"/>
<property name="artifact.output.seurat:testing_jar" value="${basedir}/../../../../../../Volumes/ngd-data/Craig_lab/alexischr/new_home/tests/seurat_snv/bin"/>
<mkdir dir="${artifacts.temp.dir}"/>
<property name="temp.jar.path.Seurat.jar" value="${artifacts.temp.dir}/Seurat.jar"/>
<property name="temp.jar.path.Seurat.jar2" value="${artifacts.temp.dir}/1/Seurat.jar"/>
<mkdir dir="${artifacts.temp.dir}/1"/>
</target>
<target name="artifact.seurat:jar" depends="init.artifacts, compile.module.seurat" description="Build 'Seurat:jar' artifact">
<property name="artifact.temp.output.seurat:jar" value="${artifacts.temp.dir}/Seurat_jar"/>
<mkdir dir="${artifact.temp.output.seurat:jar}"/>
<jar destfile="${temp.jar.path.Seurat.jar}" duplicate="preserve" filesetmanifest="mergewithoutmain">
<zipfileset file="${basedir}/Seurat/src/META-INF/MANIFEST.MF" prefix="META-INF"/>
<zipfileset dir="${seurat.output.dir}"/>
<zipfileset src="${basedir}/lib/jsc.jar"/>
<zipfileset src="${basedir}/lib/GenomeAnalysisTK-1.5-32-g2761da9/GenomeAnalysisTK.jar"/>
</jar>
<copy file="${temp.jar.path.Seurat.jar}" tofile="${artifact.temp.output.seurat:jar}/Seurat.jar"/>
</target>
<target name="artifact.seurat:testing_jar" depends="init.artifacts, compile.module.seurat" description="Build 'Seurat:testing_jar' artifact">
<property name="artifact.temp.output.seurat:testing_jar" value="${artifacts.temp.dir}/Seurat_testing_jar"/>
<mkdir dir="${artifact.temp.output.seurat:testing_jar}"/>
<jar destfile="${temp.jar.path.Seurat.jar2}" duplicate="preserve" filesetmanifest="mergewithoutmain">
<zipfileset file="${basedir}/Seurat/src/META-INF/MANIFEST.MF" prefix="META-INF"/>
<zipfileset dir="${seurat.output.dir}"/>
<zipfileset src="${basedir}/lib/jsc.jar"/>
<zipfileset src="${basedir}/lib/GenomeAnalysisTK-1.5-32-g2761da9/GenomeAnalysisTK.jar"/>
<zipfileset src="${basedir}/lib/commons-math3-3.2.jar"/>
</jar>
<copy file="${temp.jar.path.Seurat.jar2}" tofile="${artifact.temp.output.seurat:testing_jar}/Seurat.jar"/>
</target>
<target name="build.all.artifacts" depends="artifact.seurat:jar" description="Build all artifacts">
<mkdir dir="${artifact.output.seurat:jar}"/>
<copy todir="${artifact.output.seurat:jar}">
<fileset dir="${artifact.temp.output.seurat:jar}"/>
</copy>
<!-- Delete temporary files -->
<delete dir="${artifacts.temp.dir}"/>
</target>
<target name="all" depends="build.modules, build.all.artifacts" description="build all"/>
</project>