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build.xml
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build.xml
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<?xml version="1.0" encoding="UTF-8"?>
<!--
~ The MIT License (MIT)
~
~ Copyright (c) 2011-2021 Broad Institute, Aiden Lab, Rice University, Baylor College of Medicine
~
~ Permission is hereby granted, free of charge, to any person obtaining a copy
~ of this software and associated documentation files (the "Software"), to deal
~ in the Software without restriction, including without limitation the rights
~ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
~ copies of the Software, and to permit persons to whom the Software is
~ furnished to do so, subject to the following conditions:
~
~ The above copyright notice and this permission notice shall be included in
~ all copies or substantial portions of the Software.
~
~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
~ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
~ FITNESS FOR A PARTICULAR PURPOSE AND NON-INFRINGEMENT. IN NO EVENT SHALL THE
~ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
~ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
~ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
~ THE SOFTWARE.
-->
<project name="juicebox" default="all">
<property file="juicebox.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="-Xlint:all -target 1.8"/>
<property name="compiler.max.memory" value="700m"/>
<patternset id="ignored.files">
<exclude name="**/*.hprof/**"/>
<exclude name="**/*.pyc/**"/>
<exclude name="**/*.pyo/**"/>
<exclude name="**/*.rbc/**"/>
<exclude name="**/*~/**"/>
<exclude name="**/.DS_Store/**"/>
<exclude name="**/.bundle/**"/>
<exclude name="**/.git/**"/>
<exclude name="**/.hg/**"/>
<exclude name="**/.svn/**"/>
<exclude name="**/.tox/**"/>
<exclude name="**/CVS/**"/>
<exclude name="**/RCS/**"/>
<exclude name="**/SCCS/**"/>
<exclude name="**/__pycache__/**"/>
<exclude name="**/_svn/**"/>
<exclude name="**/rcs/**"/>
<exclude name="**/vssver.scc/**"/>
<exclude name="**/vssver2.scc/**"/>
</patternset>
<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"/>
<include name="**/?*.txt"/>
<include name="**/?*.sizes"/>
<include name="**/?*.cu"/>
</patternset>
<!-- JDK definitions -->
<property name="jdk.bin.1.8" value="${jdk.home.1.8}/bin"/>
<path id="jdk.classpath.1.8">
<fileset dir="${jdk.home.1.8}">
<include name="lib/ant-javafx.jar"/>
<include name="lib/dt.jar"/>
<include name="lib/javafx-mx.jar"/>
<include name="lib/jconsole.jar"/>
<include name="lib/sa-jdi.jar"/>
<include name="lib/tools.jar"/>
<include name="jre/lib/charsets.jar"/>
<include name="jre/lib/deploy.jar"/>
<include name="jre/lib/javaws.jar"/>
<include name="jre/lib/jce.jar"/>
<include name="jre/lib/jfr.jar"/>
<include name="jre/lib/jfxswt.jar"/>
<include name="jre/lib/jsse.jar"/>
<include name="jre/lib/management-agent.jar"/>
<include name="jre/lib/plugin.jar"/>
<include name="jre/lib/resources.jar"/>
<include name="jre/lib/rt.jar"/>
<include name="jre/lib/ext/cldrdata.jar"/>
<include name="jre/lib/ext/dnsns.jar"/>
<include name="jre/lib/ext/jfxrt.jar"/>
<include name="jre/lib/ext/localedata.jar"/>
<include name="jre/lib/ext/nashorn.jar"/>
<include name="jre/lib/ext/sunec.jar"/>
<include name="jre/lib/ext/sunjce_provider.jar"/>
<include name="jre/lib/ext/sunpkcs11.jar"/>
<include name="jre/lib/ext/zipfs.jar"/>
</fileset>
</path>
<property name="project.jdk.home" value="${jdk.home.1.8}"/>
<property name="project.jdk.bin" value="${jdk.bin.1.8}"/>
<property name="project.jdk.classpath" value="jdk.classpath.1.8"/>
<!-- Project Libraries -->
<path id="library.broadinstitute.classpath">
<fileset dir="${basedir}/lib/broadinstitute">
<patternset refid="library.patterns"/>
</fileset>
</path>
<path id="library.general.classpath">
<fileset dir="${basedir}/lib/general">
<patternset refid="library.patterns"/>
</fileset>
</path>
<path id="library.jcuda.classpath">
<fileset dir="${basedir}/lib/jcuda">
<patternset refid="library.patterns"/>
</fileset>
</path>
<path id="library.kotlin.classpath">
<fileset dir="${basedir}/lib/kotlin">
<patternset refid="library.patterns"/>
</fileset>
</path>
<path id="library.math3.classpath">
<pathelement location="${basedir}/lib/general/commons-math3-3.6.1.jar"/>
</path>
<path id="library.jsi1.1.classpath">
<pathelement location="${basedir}/lib/general/jsi1.1.jar"/>
</path>
<!-- Modules -->
<!-- Module Juicebox -->
<dirname property="module.juicebox.basedir" file="${ant.file}"/>
<property name="module.jdk.home.juicebox" value="${project.jdk.home}"/>
<property name="module.jdk.bin.juicebox" value="${project.jdk.bin}"/>
<property name="module.jdk.classpath.juicebox" value="${project.jdk.classpath}"/>
<property name="compiler.args.juicebox" value="-encoding UTF-8 -source 1.8 ${compiler.args}"/>
<property name="juicebox.output.dir" value="${module.juicebox.basedir}/out/production/Juicebox"/>
<property name="juicebox.testoutput.dir" value="${module.juicebox.basedir}/out/test/Juicebox"/>
<path id="juicebox.module.bootclasspath">
<!-- Paths to be included in compilation bootclasspath -->
<pathelement location="${jdk.home.1.8}/jre/lib"/>
</path>
<path id="juicebox.module.production.classpath">
<path refid="${module.jdk.classpath.juicebox}"/>
<path refid="library.broadinstitute.classpath"/>
<path refid="library.jcuda.classpath"/>
<path refid="library.kotlin.classpath"/>
<path refid="library.general.classpath"/>
<path refid="library.jsi1.1.classpath"/>
<path refid="library.math3.classpath"/>
</path>
<path id="juicebox.runtime.production.module.classpath">
<pathelement location="${juicebox.output.dir}"/>
<path refid="library.broadinstitute.classpath"/>
<path refid="library.jcuda.classpath"/>
<path refid="library.kotlin.classpath"/>
<path refid="library.general.classpath"/>
<path refid="library.jsi1.1.classpath"/>
<path refid="library.math3.classpath"/>
</path>
<path id="juicebox.module.classpath">
<path refid="${module.jdk.classpath.juicebox}"/>
<pathelement location="${juicebox.output.dir}"/>
<path refid="library.broadinstitute.classpath"/>
<path refid="library.jcuda.classpath"/>
<path refid="library.kotlin.classpath"/>
<path refid="library.general.classpath"/>
<path refid="library.jsi1.1.classpath"/>
<path refid="library.math3.classpath"/>
</path>
<path id="juicebox.runtime.module.classpath">
<pathelement location="${juicebox.testoutput.dir}"/>
<pathelement location="${juicebox.output.dir}"/>
<path refid="library.broadinstitute.classpath"/>
<path refid="library.jcuda.classpath"/>
<path refid="library.kotlin.classpath"/>
<path refid="library.general.classpath"/>
<path refid="library.jsi1.1.classpath"/>
<path refid="library.math3.classpath"/>
</path>
<patternset id="excluded.from.module.juicebox">
<patternset refid="ignored.files"/>
</patternset>
<patternset id="excluded.from.compilation.juicebox">
<patternset refid="excluded.from.module.juicebox"/>
</patternset>
<path id="juicebox.module.sourcepath">
<dirset dir="${module.juicebox.basedir}">
<include name="src"/>
</dirset>
</path>
<target name="compile.module.juicebox" depends="compile.module.juicebox.production,compile.module.juicebox.tests"
description="Compile module Juicebox"/>
<target name="compile.module.juicebox.production" description="Compile module Juicebox; production classes">
<mkdir dir="${juicebox.output.dir}"/>
<javac includeantruntime="false" destdir="${juicebox.output.dir}" debug="${compiler.debug}"
nowarn="${compiler.generate.no.warnings}" memorymaximumsize="${compiler.max.memory}" fork="true"
executable="${module.jdk.bin.juicebox}/javac">
<compilerarg line="${compiler.args.juicebox}"/>
<bootclasspath refid="juicebox.module.bootclasspath"/>
<classpath refid="juicebox.module.production.classpath"/>
<src refid="juicebox.module.sourcepath"/>
<patternset refid="excluded.from.compilation.juicebox"/>
</javac>
<copy todir="${juicebox.output.dir}">
<fileset dir="${module.juicebox.basedir}/src">
<patternset refid="compiler.resources"/>
<type type="file"/>
</fileset>
</copy>
</target>
<target name="compile.module.juicebox.tests" depends="compile.module.juicebox.production"
description="compile module Juicebox; test classes" unless="skip.tests"/>
<target name="clean.module.juicebox" description="cleanup module">
<delete dir="${juicebox.output.dir}"/>
<delete dir="${juicebox.testoutput.dir}"/>
</target>
<target name="init" description="Build initialization">
<!-- Perform any build initialization in this target -->
</target>
<target name="clean" depends="clean.module.juicebox" description="cleanup all"/>
<target name="build.modules" depends="init, clean, compile.module.juicebox" description="build all modules"/>
<target name="init.artifacts">
<property name="artifacts.temp.dir" value="${basedir}/__artifacts_temp"/>
<property name="artifact.output.juicebox:jar" value="${basedir}/out/artifacts/Juicebox_jar"/>
<property name="artifact.output.juicer_tools:jar" value="${basedir}/out/artifacts/juicer_tools_jar"/>
<mkdir dir="${artifacts.temp.dir}"/>
<property name="temp.jar.path.Juicebox.jar" value="${artifacts.temp.dir}/Juicebox.jar"/>
<property name="temp.jar.path.juicer_tools.jar" value="${artifacts.temp.dir}/1/juicer_tools.jar"/>
<mkdir dir="${artifacts.temp.dir}/1"/>
</target>
<target name="artifact.juicebox:jar" depends="init.artifacts, compile.module.juicebox"
description="Build 'Juicebox:jar' artifact">
<property name="artifact.temp.output.juicebox:jar" value="${artifacts.temp.dir}/Juicebox_jar"/>
<mkdir dir="${artifact.temp.output.juicebox:jar}"/>
<jar destfile="${temp.jar.path.Juicebox.jar}" duplicate="preserve"
manifest="${basedir}/src/resources/manifests/juicebox_jar/META-INF/MANIFEST.MF">
<zipfileset file="${basedir}/src/resources/manifests/juicebox_jar/META-INF/MANIFEST.MF" prefix="META-INF"/>
<zipfileset dir="${juicebox.output.dir}"/>
<zipfileset src="${basedir}/lib/general/jsi1.1.jar" excludes="META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA"/>
<zipfileset src="${basedir}/lib/broadinstitute/igv.jar" excludes="META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA"/>
<zipfileset src="${basedir}/lib/broadinstitute/htsjdk-1.139.jar"/>
<zipfileset src="${basedir}/lib/broadinstitute/log4j-core-2.11.0.jar"
excludes="META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA"/>
<zipfileset src="${basedir}/lib/jcuda/jcuda-0.8.0.jar"/>
<zipfileset src="${basedir}/lib/jcuda/jcuda-natives-0.8.0-linux-ppc_64.jar"/>
<zipfileset src="${basedir}/lib/jcuda/jcuda-natives-0.8.0-linux-x86_64.jar"/>
<zipfileset src="${basedir}/lib/jcuda/jcuda-natives-0.8.0-apple-x86_64.jar"/>
<zipfileset src="${basedir}/lib/jcuda/jcudaUtils-0.0.4.jar"/>
<zipfileset src="${basedir}/lib/general/guava-18.0.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-reflect-sources.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-reflect.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-stdlib-jdk7-sources.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-stdlib-jdk7.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-stdlib-jdk8-sources.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-stdlib-jdk8.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-stdlib-sources.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-stdlib.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-test-sources.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-test.jar"/>
<zipfileset src="${basedir}/lib/general/VectorGraphics2D-0.11.jar"/>
<zipfileset src="${basedir}/lib/general/jargs.jar" excludes="META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA"/>
<zipfileset src="${basedir}/lib/general/jfreechart-1.0.19.jar" excludes="META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA"/>
</jar>
<copy file="${temp.jar.path.Juicebox.jar}" tofile="${artifact.temp.output.juicebox:jar}/Juicebox.jar"/>
</target>
<target name="artifact.juicer_tools:jar" depends="init.artifacts, compile.module.juicebox"
description="Build 'juicer_tools:jar' artifact">
<property name="artifact.temp.output.juicer_tools:jar" value="${artifacts.temp.dir}/juicer_tools_jar"/>
<mkdir dir="${artifact.temp.output.juicer_tools:jar}"/>
<jar destfile="${temp.jar.path.juicer_tools.jar}" duplicate="preserve"
manifest="/resources/MANIFEST.MF">
<zipfileset file="/resources/MANIFEST.MF"
prefix="META-INF"/>
<zipfileset dir="${juicebox.output.dir}"/>
<zipfileset src="${basedir}/lib/general/jsi1.1.jar" excludes="META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA"/>
<zipfileset src="${basedir}/lib/general/commons-math3-3.6.1.jar"/>
<zipfileset src="${basedir}/lib/general/guava-18.0.jar"/>
<zipfileset src="${basedir}/lib/general/VectorGraphics2D-0.11.jar"/>
<zipfileset src="${basedir}/lib/broadinstitute/igv.jar"
excludes="META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA"/>
<zipfileset src="${basedir}/lib/broadinstitute/htsjdk-1.139.jar"/>
<zipfileset src="${basedir}/lib/broadinstitute/log4j-core-2.11.0.jar"
excludes="META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA"/>
<zipfileset src="${basedir}/lib/jcuda/jcuda-0.8.0.jar"/>
<zipfileset src="${basedir}/lib/jcuda/jcuda-natives-0.8.0-linux-ppc_64.jar"/>
<zipfileset src="${basedir}/lib/jcuda/jcuda-natives-0.8.0-linux-x86_64.jar"/>
<zipfileset src="${basedir}/lib/jcuda/jcuda-natives-0.8.0-apple-x86_64.jar"/>
<zipfileset src="${basedir}/lib/jcuda/jcudaUtils-0.0.4.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-reflect-sources.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-reflect.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-stdlib-jdk7-sources.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-stdlib-jdk7.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-stdlib-jdk8-sources.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-stdlib-jdk8.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-stdlib-sources.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-stdlib.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-test-sources.jar"/>
<zipfileset src="${basedir}/lib/kotlin/kotlin-test.jar"/>
<zipfileset src="${basedir}/lib/general/jargs.jar" excludes="META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA"/>
<zipfileset src="${basedir}/lib/general/jfreechart-1.0.19.jar"
excludes="META-INF/*.SF,META-INF/*.DSA,META-INF/*.RSA"/>
</jar>
<copy file="${temp.jar.path.juicer_tools.jar}"
tofile="${artifact.temp.output.juicer_tools:jar}/juicer_tools.jar"/>
</target>
<target name="sign">
<signjar
alias="${sign.alias}" keystore="${sign.keystore}" storepass="${sign.storepass}"
tsaurl="http://timestamp.digicert.com">
<path>
<fileset dir="${basedir}/out" includes="**/*.jar"/>
</path>
</signjar>
</target>
<target name="build.all.artifacts" depends="artifact.juicebox:jar, artifact.juicer_tools:jar"
description="Build all artifacts">
<mkdir dir="${artifact.output.juicebox:jar}"/>
<copy todir="${artifact.output.juicebox:jar}">
<fileset dir="${artifact.temp.output.juicebox:jar}"/>
</copy>
<mkdir dir="${artifact.output.juicer_tools:jar}"/>
<copy todir="${artifact.output.juicer_tools:jar}">
<fileset dir="${artifact.temp.output.juicer_tools:jar}"/>
</copy>
<!-- Delete temporary files -->
<delete dir="${artifacts.temp.dir}"/>
</target>
<target name="juicer_tools" depends="artifact.juicer_tools:jar" description="Build juicer_tools artifact">
<mkdir dir="${artifact.output.juicer_tools:jar}"/>
<copy todir="${artifact.output.juicer_tools:jar}">
<fileset dir="${artifact.temp.output.juicer_tools:jar}"/>
</copy>
<!-- Delete temporary files -->
<delete dir="${artifacts.temp.dir}"/>
</target>
<target name="all" depends="build.modules, build.all.artifacts" description="build all"/>
<taskdef name="jarbundler"
classname="com.ultramixer.jarbundler.JarBundler"
classpath="lib/jarbundler-core-3.3.0.jar"/>
<target name="bundle" depends="init.artifacts">
<property name="version" value="1.0 (1)"/>
<jarbundler dir="${artifact.output.juicebox:jar}"
name="Juicebox"
mainclass="juicebox.MainWindow"
icon="JuiceboxIcon.icns"
jar="${artifact.output.juicebox:jar}/Juicebox.jar"
stubfile="lib/universalJavaApplicationStub"
useJavaXKey="true"
jvmversion="1.8"
version="${version}"
highResolutionCapable="true"
bundleid="org.aidenlab.Juicebox"
copyright="©2014, Broad Institute and Aiden Lab"
vmoptions="-Xms5g -Xmx10g -d64">
</jarbundler>
<delete dir="${artifacts.temp.dir}"/>
</target>
<target name="bundlebcm" depends="init.artifacts">
<property name="version" value="1.0 (1)"/>
<jarbundler dir="${artifact.output.juicebox:jar}"
name="Juicebox"
mainclass="juicebox.MainWindow"
icon="JuiceboxIcon.icns"
jar="${artifact.output.juicebox:jar}/Juicebox.jar"
stubfile="lib/universalJavaApplicationStub"
useJavaXKey="true"
jvmversion="1.8"
version="${version}"
highResolutionCapable="true"
copyright="©2014, Broad Institute and Aiden Lab"
vmoptions="-Xms5g -Xmx10g -d64">
</jarbundler>
<delete dir="${artifacts.temp.dir}"/>
</target>
</project>