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<?xml version="1.0" encoding="UTF-8"?>
<project name="BeagleSequenceSimulator" default="help" basedir=".">
<property name="build.sysclasspath" value="last" />
<property name="Main-Class" value="dr.app.bss.BeagleSequenceSimulatorApp" />
<property name="JDK_VERSION" value="1.6" />
<property name="src" location="src"/>
<property name="build" location="build" />
<property name="dist" location="dist" />
<property name="lib" location="lib" />
<target name="help">
<echo message="Common build targets:" />
<echo message="jar - Builds buss.jar" />
<echo message="build - Same as clean+jar" />
<echo message="compile - Compiles buss classes" />
<echo message="clean - Remove all *.class and buss.jar" />
</target>
<path id="classpath">
<fileset dir="${lib}" includes="**/*.jar"/>
</path>
<target name="build" depends="clean,jar" />
<target name="jar" depends="compile">
<mkdir dir="${dist}" />
<jar jarfile="${dist}/buss.jar">
<manifest>
<attribute name="Built-By" value="${user.name}" />
<attribute name="Main-Class" value="${Main-Class}" />
</manifest>
<fileset dir="${build}">
<include name="dr/app/bss/**/*.class" />
<include name="dr/inference/model/**/*.class" />
<include name="dr/inference/loggers/**/*.class" />
<include name="dr/inference/distribution/**/*.class" />
<include name="dr/evomodel/branchratemodel/**/*.class" />
<include name="dr/evomodel/branchmodel/**/*.class" />
<include name="dr/evomodel/substmodel/**/*.class" />
<include name="dr/app/beagle/evomodel/substmodel/**/*.class" />
<include name="dr/app/beagle/evomodel/branchmodel/**/*.class" />
<include name="dr/inference/parallel/**/*.class**" />
<include name="dr/app/beagle/evomodel/sitemodel/**/*.class" />
<include name="dr/app/beauti/options/**/*.class" />
<include name="dr/app/beauti/tipdatepanel/**/*.class" />
<include name="dr/app/gui/table/**/*.class" />
<include name="dr/app/gui/components/**/*.class" />
<include name="dr/app/beauti/util/**/*.class" />
<include name="dr/evomodel/tree/**/*.class" />
<include name="dr/app/beagle/tools/**/*.class" />
<include name="dr/app/beagle/evomodel/treelikelihood/**/*.class" />
<include name="dr/app/beagle/evomodel/treelikelihood/**/*.class" />
<include name="dr/app/util/**/*.class" />
<include name="dr/evolution/alignment/**/*.class" />
<include name="dr/evolution/coalescent/**/*.class" />
<include name="dr/evolution/colouring/**/*.class" />
<include name="dr/evolution/datatype/**/*.class" />
<include name="dr/evolution/distance/**/*.class" />
<include name="dr/evolution/io/**/*.class" />
<include name="dr/evolution/parsimony/**/*.class" />
<include name="dr/evolution/sequence/**/*.class" />
<include name="dr/evolution/tree/**/*.class" />
<include name="dr/evolution/util/**/*.class" />
<include name="dr/evoxml/**/*.class" />
<include name="dr/gui/table/**/*.class" />
<include name="dr/inference/trace/**/*.class" />
<include name="dr/math/**/*.class" />
<include name="dr/matrix/**/*.class" />
<include name="dr/stats/**/*.class" />
<include name="dr/util/**/*.class" />
<include name="dr/xml/**/*.class" />
<include name="dr/evomodelxml/branchratemodel/**/*.class" />
<include name="dr/evomodelxml/coalescent/**/*.class" />
<include name="dr/evomodelxml/sitemodel/**/*.class" />
<include name="dr/evomodelxml/tree/**/*.class" />
<include name="dr/app/beagle/tools/parsers/**/*.class" />
<include name="dr/evolution/io/Importer/**/*.class" />
</fileset>
<zipgroupfileset dir="${lib}" includes="jam.jar" />
<zipgroupfileset dir="${lib}" includes="beagle.jar" />
<zipgroupfileset dir="${lib}" includes="commons-math-2.2.jar" />
<fileset dir="${src}">
<include name="dr/**/*.png"/>
</fileset>
</jar>
</target>
<target name="compile">
<mkdir dir="${build}" />
<javac source="${JDK_VERSION}" target="${JDK_VERSION}" srcdir="${src}" destdir="${build}" classpathref="classpath">
<include name="dr/app/bss/**" />
<include name="dr/inference/model/**" />
<include name="dr/inference/loggers/**" />
<include name="dr/inference/distribution/**" />
<include name="dr/evomodel/branchratemodel/**" />
<include name="dr/evomodel/branchmodel/**" />
<include name="dr/evomodel/substmodel/**" />
<include name="dr/app/beagle/evomodel/substmodel/**" />
<include name="dr/app/beagle/evomodel/branchmodel/**" />
<include name="dr/inference/parallel/**" />
<include name="dr/app/beagle/evomodel/sitemodel/**" />
<include name="dr/app/beauti/options/**" />
<include name="dr/app/beauti/tipdatepanel/**" />
<include name="dr/app/gui/table/**" />
<include name="dr/app/gui/components/**" />
<include name="dr/app/beauti/util/**" />
<include name="dr/evomodel/tree/**" />
<include name="dr/app/beagle/tools/**" />
<include name="dr/app/beagle/evomodel/treelikelihood/**" />
<include name="dr/app/util/**" />
<include name="dr/evolution/alignment/**" />
<include name="dr/evolution/colouring/**" />
<include name="dr/evolution/datatype/**" />
<include name="dr/evolution/distance/**" />
<include name="dr/evolution/io/**" />
<include name="dr/evolution/parsimony/**" />
<include name="dr/evolution/sequence/**" />
<include name="dr/evolution/tree/**" />
<include name="dr/evolution/util/**" />
<include name="dr/evoxml/**" />
<include name="dr/gui/table/**" />
<include name="dr/inference/trace/**" />
<include name="dr/math/**" />
<include name="dr/matrix/**" />
<include name="dr/stats/**" />
<include name="dr/util/**" />
<include name="dr/xml/**" />
<include name="dr/evomodelxml/branchratemodel/**" />
<include name="dr/evomodelxml/coalescent/**" />
<include name="dr/evomodelxml/sitemodel/**" />
<include name="dr/evomodelxml/tree/**" />
<include name="dr/app/beagle/tools/parsers/**" />
<include name="dr/evolution/io/Importer/**" />
</javac>
<echo message="Successfully compiled." />
</target>
<property name="version" value="1.4" />
<property name="release_dir" value="release_pibuss" />
<property name="name" value="piBUSS" />
<property name="common_dir" value="${release_dir}/common" />
<property name="Mac_dir" value="${release_dir}/Mac" />
<property name="Linux_dir" value="${release_dir}/Linux" />
<property name="Windows_dir" value="${release_dir}/Windows" />
<property name="Mac_package_dir" value="${Mac_dir}/${name} v${version}" />
<property name="Linux_package_dir" value="${Linux_dir}/${name}_v${version}" />
<property name="Windows_package_dir" value="${Windows_dir}/${name} v${version}" />
<!-- Need to either install Launch4j under {BEAST workspace}/${release}
or install it in the default directory and change the location of launch4j.dir -->
<target name="windows" depends="build" description="release Windows version of πBUSS">
<delete dir="${Windows_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Windows_package_dir}" />
<property name="launch4j.dir" location="${Windows_dir}/launch4j" />
<taskdef name="launch4j" classname="net.sf.launch4j.ant.Launch4jTask"
classpath="${launch4j.dir}/launch4j.jar :${launch4j.dir}/lib/xstream.jar" />
<copy file="${dist}/buss.jar" todir="${Windows_package_dir}/lib"/>
<copy todir="${Windows_package_dir}/lib">
<fileset dir="${Windows_dir}/lib"/>
</copy>
<copy file="${common_dir}/README.txt" todir="${Windows_package_dir}"/>
<launch4j configFile="${Windows_dir}/pibuss_launch4j.xml"
jar="${dist}/buss.jar"
outfile="${Windows_package_dir}/${name} v${version}.exe"
fileVersion="${version}.0.0"
txtFileVersion="${version}"
productVersion="${version}.0.0"
txtProductVersion="${version}"/>
<zip destfile="${release_dir}/${name} v${version}.zip">
<zipfileset dir="${Windows_package_dir}" prefix="${name} v${version}"/>
</zip>
<echo message="Windows version release is finished." />
</target>
<target name="linux" depends="build" description="release Linux/Unix version of πBUSS">
<delete dir="${Linux_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Linux_package_dir}" />
<mkdir dir="${Linux_dir}/lib" />
<copy todir="${Linux_package_dir}/bin">
<fileset dir="${Linux_dir}/scripts"/>
</copy>
<chmod dir="${Linux_package_dir}/bin" perm="755" includes="**/**"/>
<copy file="${Linux_dir}/icons/pibuss.png" todir="${Linux_package_dir}/images"/>
<copy file="${dist}/buss.jar" todir="${Linux_package_dir}/lib"/>
<copy todir="${Linux_package_dir}/lib">
<fileset dir="${Linux_dir}/lib"/>
</copy>
<copy file="${common_dir}/README.txt" todir="${Linux_package_dir}"/>
<tar destfile="${release_dir}/${name}_v${version}.tgz" compression="gzip">
<tarfileset dir="${Linux_package_dir}" prefix="${name}_v${version}"/>
</tar>
<echo message="Linux/Unix version release is finished." />
</target>
<target name="mac" depends="build" description="release Mac version of πBUSS">
<delete dir="${Mac_package_dir}" />
<!-- Create the release directory -->
<mkdir dir="${Mac_package_dir}" />
<copy file="${common_dir}/README.txt" todir="${Mac_package_dir}"/>
<taskdef name="jarbundler" classname="net.sourceforge.jarbundler.JarBundler"/>
<!-- create a jar bundle for the mac -->
<jarbundler dir="${Mac_package_dir}"
name="${name} v${version}"
mainclass="dr.app.bss.BeagleSequenceSimulatorApp"
icon="${Mac_dir}/icons/πBUSS.icns"
jvmversion="1.6+"
arguments=""
version="${version}"
infostring="${name} v${version}, Copyright 2013, Filip Bielejec, Andrew Rambaut, Philippe Lemey and Marc Suchard"
bundleid="pibuss" >
<javaproperty name="apple.laf.useScreenMenuBar" value="true"/>
<jarfileset dir="${dist}">
<include name="**/buss.jar"/>
</jarfileset>
<jarfileset dir="${Mac_dir}/lib">
<include name="**/*.jar"/>
</jarfileset>
</jarbundler>
<echo message="Building disk image." />
<!-- create disk image -->
<exec executable="/usr/bin/hdiutil">
<arg value="create"/>
<arg value="-ov"/>
<arg value="-srcfolder"/>
<arg value="${Mac_package_dir}"/>
<arg value="-volname"/>
<arg value="${name} v${version}"/>
<arg value="-imagekey"/>
<arg value="zlib-level=6"/>
<arg value="${release_dir}/${name} v${version}.dmg"/>
</exec>
<echo message="Mac version release is finished." />
</target>
<target name="clean">
<delete dir="${build}" />
<delete dir="${dist}" />
</target>
</project>
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