build_coalsim.xml

<project name="CoalGen" default="all" basedir=".">
    <description>
        Build file for CoalGen versions
        $Id: build_release.xml,v 1.5 2006/09/09 18:16:17 rambaut Exp $
    </description>
    <!-- set global properties for this build -->
    <property name="src" location="src"/>
    <property name="build" location="build"/>
    <property name="lib" location="lib"/>
    <property name="dist" location="dist"/>

    <property name="JDK_VERSION" value="1.8" />

    <property environment="env"/>

    <target name="init">
        <!-- Create the time stamp -->
        <tstamp/>
        <!-- Create the build directory structure used by compile -->
        <mkdir dir="${build}"/>
        <mkdir dir="${dist}"/>
    </target>

    <target name="all"
            depends="compile-all"
            description="Build all run-time stuff">
    </target>

    <target name="compile-all"
            depends="compile-basic">
    </target>

    <path id="classpath">
		<fileset dir="${lib}" includes="**/*.jar"/>
	</path>

    <target name="compile-basic" depends="init">
        <!-- Compile the java code from ${src} into ${build} -->
        <javac source="${JDK_VERSION}" target="${JDK_VERSION}" srcdir="${src}" destdir="${build}"
               classpathref="classpath">
            <include name="dr/app/coalgen/**"/>
            <include name="dr/app/util/**"/>
            <include name="dr/evolution/alignment/**"/>
            <include name="dr/evolution/coalescent/**"/>
            <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/**"/>
        </javac>
    </target>

    <target name="dist" depends="compile-all"
            description="generate the distribution">
        <!-- Create the distribution directory -->
        <mkdir dir="${dist}"/>

        <!-- Put everything in ${build} into the treestat.jar file -->
        <jar jarfile="${dist}/coalgen.jar">
            <manifest>
                <attribute name="Built-By" value="${user.name}"/>
                <attribute name="Main-Class" value="dr.app.coalgen.CoalGenApp"/>
            </manifest>
            <fileset dir="${build}">
                <include name="dr/app/coalgen/**/*.class"/>
                <include name="dr/app/beauti/**/*.class"/>
                <include name="dr/app/gui/**/*.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"/>
            </fileset>
            <fileset dir="">
                <include name="images/*.png"/>
            </fileset>
            <fileset dir="${src}">
                <include name="dr/**/*.png"/>
            </fileset>
            <zipgroupfileset dir="${lib}" includes="**/jebl.jar"/>
            <zipgroupfileset dir="${lib}" includes="**/jam.jar"/>
            <zipgroupfileset dir="${lib}" includes="**/commons-math-2.2.jar"/>
        </jar>
    </target>
</project>