Generic ANT bulid file for BEAST 2 packages. Copy this into an otherwise empty directory and type "ant skeleton" to create a new package.

build.xml

<project default="build" basedir=".">

    <!-- Source, JUnit test code and jar library locations. -->
    <property name="src" location="src"/>
    <property name="test" location="test"/>
    <property name="lib" location="lib"/>

    <!-- Location to check for local copy of beast2 repository -->
    <property name="beastDir" location="../beast2"/>

    <!-- BEAST 2 currently uses Java 1.8 -->
    <property name="sourceVersion" value="1.8"/>
    <property name="targetVersion" value="1.8"/>

    <!-- Directories necessary for all BEAST 2 packages -->
    <property name="doc" location="doc"/>
    <property name="examples" location="examples"/>
    <property name="templates" location="templates"/>

    <!-- BEAST branch and version to build against
         (only different for version tags because of
         a Github peculiarity) -->
    <property name="beast-branch" value="master"/>
    <property name="beast-version" value="master"/>

    <!-- Names of temporary build/test directories -->
    <property name="build" location="build"/>
    <property name="build-lib" location="build-lib"/>
    <property name="build-test" location="build-test"/>
    <property name="test-reports" location="test-reports"/>
    <property name="dist" location="dist"/>
    <property name="pack" location="${dist}/package"/>

    <!-- Prepare for compilation -->
    <target name="init">

        <available file="version.xml" property="versionAvailable"/>
        <fail unless="versionAvailable">
            ** Required file version.xml does not exist. **
            If this is a new project, run "ant skeleton" from
            the command line to create the files required for
            your BEAST 2 package.
        </fail>

        <!-- Read package name and version from xml file -->
        <xmlproperty file="version.xml" prefix="fromVersionFile" />
        <property name="projName" value="${fromVersionFile.addon(name)}" />
        <property name="projVersion" value="${fromVersionFile.addon(version)}" />

        <mkdir dir="${build}"/>
        <mkdir dir="${build-lib}"/>
        <mkdir dir="${dist}"/>

        <copy todir="${build-lib}" failonerror="false" quiet="true">
            <fileset dir="${lib}" includes="*.jar"/>
        </copy>
    </target>

    <!-- Get beast -->

    <target name="find-beast" depends="init">
        <available file="${beastDir}" property="localBeastAvailable"/>
    </target>

    <target name="build-remote-beast" depends="find-beast" unless="localBeastAvailable">
        <echo>No local copy of the beast2 source found at ${beastDir}.</echo>
        <echo>Compiling against version ${beast-version} from GitHub.</echo>

        <property name="build-beast" location="build-beast"/>
        <mkdir dir="${build-beast}"/>

        <get src="https://github.com/CompEvol/beast2/archive/${beast-branch}.zip" dest="${build-beast}/beast.zip"/>
        <unzip src="${build-beast}/beast.zip" dest="${build-beast}"/>
        <mkdir dir="${build-beast}/beast2-${beast-version}/build"/>
        <javac target="${targetVersion}" source="${sourceVersion}"
            srcdir="${build-beast}/beast2-${beast-version}/src"
            destdir="${build-beast}/beast2-${beast-version}/build" includeantruntime="false">
            <classpath>
                <pathelement path="${classpath}"/>
                <fileset dir="${build-beast}/beast2-${beast-version}/lib" includes="*.jar"/>
            </classpath>
        </javac>
        <jar jarfile="${build-lib}/beast2.jar" basedir="${build-beast}/beast2-${beast-version}/build" />
        <copy todir="${build-lib}">
            <fileset dir="${build-beast}/beast2-${beast-version}/lib" includes="*.jar"/>
        </copy>

        <delete dir="${build-beast}" />
    </target>

    <target name="build-local-beast" depends="find-beast" if="localBeastAvailable">
        <echo>Compiling against beast2 source found at ${beastDir}.</echo>

        <property name="build-beast" location="build-beast"/>
        <mkdir dir="${build-beast}"/>

        <javac target="${targetVersion}" source="${sourceVersion}"
            srcdir="${beastDir}/src"
            destdir="${build-beast}" includeantruntime="false">
            <classpath>
                <pathelement path="${classpath}"/>
                <fileset dir="${beastDir}/lib" includes="*.jar"/>
            </classpath>
        </javac>
        <jar jarfile="${build-lib}/beast2.jar" basedir="${build-beast}" />
        <copy todir="${build-lib}">
            <fileset dir="${beastDir}/lib" includes="*.jar"/>
        </copy>

        <delete dir="${build-beast}" />
    </target>

    <target name="build-beast" depends="build-local-beast,build-remote-beast"/>

    <!-- Compile -->
    <target name="compile" depends="build-beast">
        <javac target="${targetVersion}" source="${sourceVersion}" srcdir="${src}" destdir="${build}" includeantruntime="false">
            <classpath>
                <pathelement path="${classpath}"/>
                <fileset dir="${build-lib}" includes="*.jar"/>
            </classpath>
        </javac>
    </target>

    <target name="copy-resources" depends="compile">
        <copy todir="${build}">
            <fileset dir="${src}"
                     includes="**/*.png" />
        </copy>
    </target>

    <!-- Prepare for unit test compilation -->
    <target name="init-test" depends="init">
        <mkdir dir="${build-test}"/>
        <mkdir dir="${test-reports}"/>
    </target>


    <!-- Compile unit tests -->
    <target name="compile-test" depends="init-test,compile,copy-resources">
        <javac target="${targetVersion}" source="${sourceVersion}" srcdir="${test}" destdir="${build-test}" includeantruntime="false">
            <classpath>
                <pathelement path="${classpath}"/>
                <pathelement path="${build}" />
                <fileset dir="${build-lib}" includes="*.jar"/>
            </classpath>
        </javac>
    </target>


    <!-- Run unit tests -->
    <target name="test" depends="compile-test">
        <junit printsummary="yes" failureproperty="testFailed" showoutput="true">
            <classpath>
                <pathelement path="${classpath}"/>
                <pathelement path="${build}" />
                <pathelement path="${build-test}" />
                <fileset dir="${build-lib}" includes="*.jar"/>
            </classpath>
            <batchtest fork="yes" todir="${test-reports}">
                <fileset dir="${test}">
                    <include name="**/*Test.java"/>
                </fileset>
                <formatter type="plain"/>
                <!--formatter type="plain" usefile="false"/--> <!-- to screen -->
            </batchtest>
        </junit>

        <fail if="testFailed" status="1" message="Unit test failed."/>
    </target>


    <!-- Create BEAST 2 package -->
    <target name="build" depends="compile,copy-resources">
        <property name="fullName" value="${projName}.v${projVersion}"/>

        <mkdir dir="${pack}"/>
        <mkdir dir="${pack}/examples"/>
        <mkdir dir="${pack}/templates"/>
        <mkdir dir="${pack}/lib"/>
        <mkdir dir="${pack}/doc"/>

        <jar jarfile="${pack}/${fullName}.src.jar" basedir="${src}" />

        <mkdir dir="${lib}" />
        <copy todir="${pack}/lib">
            <fileset dir="${lib}" includes="*.jar" />
        </copy>
        <jar jarfile="${pack}/lib/${fullName}.jar" basedir="${build}" />

        <copy file="README.md" tofile="${pack}/README" failonerror="false" quiet="true" />
        <copy file="README.md" tofile="${pack}/README" failonerror="false" quiet="true" />
        <copy file="COPYING" todir="${pack}" />
        <copy todir="${pack}">
            <fileset dir="${lib}" includes="LICENSE*" />
        </copy>

        <mkdir dir="${examples}" />
        <copy todir="${pack}/examples">
            <fileset dir="${examples}" includes="**/*.xml" />
            <fileset dir="${examples}" includes="**/*.fasta" />
        </copy>

        <mkdir dir="${templates}" />
        <copy todir="${pack}/templates">
            <fileset dir="${templates}" includes="*.xml" />
        </copy>

        <mkdir dir="${doc}" />
        <copy todir="${pack}/doc">
            <fileset dir="${doc}" includes="*.tex,*.doc,*.lyx,*.txt"/>
        </copy>

        <copy file="version.xml" todir="${pack}" />

        <zip destfile="${dist}/${fullName}.zip" basedir="${pack}" />

        <delete dir="${pack}"/>

        <echo/>
        <echo/>
        <echo>** Package ${dist}/${fullName}.zip created successfuly! **</echo>
    </target>


    <!-- Revert to pristine state. -->
    <target name="clean">
        <delete dir="${build}" />
        <delete dir="${build-lib}" />
        <delete dir="${dist}" />
        <delete dir="${build-test}" />
        <delete dir="${test-reports}" />
    </target>


    <!-- Create skeleton package layout in current directory -->
    <target name="skeleton">

        <fail>
            <condition>
                <or>
                    <resourcecount when="gt" count="1">
                        <fileset dir="${basedir}"/>
                    </resourcecount>
                    <resourcecount when="gt" count="1">
                        <dirset dir="${basedir}"/>
                    </resourcecount>
                </or>
            </condition>

            ** This directory contains files besides the build script. **
            You should run "ant skeleton" in a directory containing only the build script.
        </fail>

        <echo>===============================</echo>
        <echo>Create skeleton BEAST 2 package</echo>
        <echo>===============================</echo>
        <echo/>
        <echo>First, we need some information...</echo>
        <echo/>

        <basename property="defaultProjName" file="${basedir}"/>

        <input addproperty="projName" defaultvalue="${defaultProjName}">Enter package name</input>
        <input addproperty="license" defaultvalue="gpl3" validargs="gpl3,lgpl3,lgpl2.1,apache2">Select open source software license</input>
        <input addproperty="projVersion" defaultvalue="1.0.0">Enter package version</input>
        <input addproperty="beastVersionReq" defaultvalue="2.4.0">Enter minimum required BEAST 2 version</input>

        <echo>Assembling files and directory structure...</echo>

        <echo file="version.xml">&lt;addon name="${projName}" version="${projVersion}"&gt;
            &lt;depends on="BEAST" atleast="${beastVersionReq}"/&gt;

            &lt;!-- Add other dependencies as necessary. --&gt;
            &lt;/addon&gt;
        </echo>

        <echo file="README.md" message="README for my package.${line.separator}"/>

        <condition property="licenseURL" value="https://www.gnu.org/licenses/gpl-3.0.txt">
            <equals arg1="${license}" arg2="gpl3"/>
        </condition>
        <condition property="licenseURL" value="https://www.gnu.org/licenses/lgpl-3.0.txt">
            <equals arg1="${license}" arg2="lgpl3"/>
        </condition>
        <condition property="licenseURL" value="https://www.gnu.org/licenses/lgpl-2.1.txt">
            <equals arg1="${license}" arg2="lgpl2.1"/>
        </condition>
        <condition property="licenseURL" value="http://www.apache.org/licenses/LICENSE-2.0.txt">
            <equals arg1="${license}" arg2="apache2"/>
        </condition>

        <get src="${licenseURL}" dest="COPYING"/>

        <mkdir dir="${src}"/>
        <mkdir dir="${test}"/>
        <mkdir dir="${lib}"/>
        <mkdir dir="${examples}"/>
        <mkdir dir="${templates}"/>
        <mkdir dir="${doc}"/>

        <echo/>
        <echo>Done.</echo>
        <echo/>
        <echo>The directory structure is as follows:</echo>
        <echo>${src} - your java source goes here</echo>
        <echo>${test} - your junit tests go here (You _are_ going to write, those, aren't you!)</echo>
        <echo>${doc} - your documentation goes here</echo>
        <echo>${examples} - your example XML scripts go here</echo>
        <echo>${templates} - your BEAUti templates go here</echo>
        <echo/>
        <echo>To build your package, just type "ant" at the command line.</echo>
        <echo/>
        <echo>To run unit tests, type "ant test".</echo>
        <echo/>
        <echo>That's it!  Happy coding!</echo>

    </target>

</project>