build.xml

<project name="ngsutilsj" default="jar">
    <property name="version" value="0.5.6"/>
    <property name="build" value="dev"/>
    <property name="lib.dir" value="lib"/>
    <property name="blib.dir" value="blib"/>
    <property name="build.dir" value="build"/>
    <property name="dist.dir" value="dist"/>
    <property name="src.dir" value="src"/>
	
    <target name="clean">
        <delete dir="${build.dir}"/>
        <delete dir="${dist.dir}"/>
    </target>

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

	<target name="compile">
        <mkdir dir="${build.dir}/classes"/>
    <!--
           <javac srcdir="${src.dir}/java" destdir="${build.dir}/classes" classpathref="classpath" debug="true" debuglevel="lines,vars,source"/>
    -->
        <javac
            srcdir="${src.dir}/java"
            destdir="${build.dir}/classes"
            encoding="UTF-8"
            debug="true"
            includeantruntime="false"
            classpathref="classpath"
            debuglevel="lines,vars,source"
        	release="8"
			>
            <!--modulepathref="classpath"-->
        			  <compilerarg value="-Xlint:-options"/>
        </javac>
    	
    </target>

	<target name="jar" depends="compile, git.revision">
        <copy file="LICENSE" todir="${build.dir}/classes/"/>
        <copy file="INCLUDES" todir="${build.dir}/classes/"/>
        <echo file="${build.dir}/classes/io/compgen/ngsutils/ngsutilsj.properties" message="build=${build}${line.separator}"/>
        <echo file="${build.dir}/classes/io/compgen/ngsutils/ngsutilsj.properties" message="version=${version}${line.separator}" append="true"/>
        <echo file="${build.dir}/classes/io/compgen/ngsutils/ngsutilsj.properties" message="gitcommit=${repository.version}${line.separator}" append="true"/>

		<mkdir dir="${dist.dir}"/>
	    <taskdef name="jarjar" classname="com.tonicsystems.jarjar.JarJarTask"
	        classpath="${blib.dir}/jarjar-1.4.jar"/>
        <jar destfile="${dist.dir}/${ant.project.name}-${version}.jar">
            <fileset dir="${build.dir}/classes"/>
            <fileset dir="${src.dir}/java" includes="**/*.java"/>
        </jar>
	    <jarjar jarfile="${dist.dir}/ngsutilsj.jar.tmp">
            <manifest>
                <attribute name="Main-Class" value="io.compgen.ngsutils.NGSUtils"/>
            </manifest>
            <fileset dir="${build.dir}/classes"/>
            <zipfileset src="${lib.dir}/htsjdk-1.126.jar"/>
            <zipfileset src="${lib.dir}/snappy-java-1.0.3-rc3.jar"/>
            <zipfileset src="${lib.dir}/commons-jexl-2.1.1.jar"/>
            <zipfileset src="${lib.dir}/commons-logging-1.1.1.jar"/>
            <zipfileset src="${lib.dir}/commons-math3-3.3.jar"/>
            <zipfileset src="${lib.dir}/compgen-common-0.4.4.jar"/>
            <zipfileset src="${lib.dir}/compgen-cmdline-0.4.5.jar"/>
            <zipfileset src="${lib.dir}/commons-compress-1.8.1.jar"/>
            <zap pattern="*.java"/>
	    </jarjar>
        <delete file="${dist.dir}/ngsutilsj"/>
 		<concat destfile="${dist.dir}/ngsutilsj" binary="true">
 		     <fileset file="${src.dir}/scripts/stub.sh" />
 		     <fileset file="${dist.dir}/ngsutilsj.jar.tmp" />
 		</concat>
        <delete file="${dist.dir}/ngsutilsj.jar.tmp"/>
		<chmod file="${dist.dir}/ngsutilsj" perm="755"/>
	</target>

	<!-- See http://stackoverflow.com/questions/2974106/how-to-lookup-the-latest-git-commit-hash-from-an-ant-build-script -->
	<available file=".git" type="dir" property="git.present"/>
	<target name="git.revision" description="Store git revision in ${repository.version}" if="git.present">
	    <exec executable="git" outputproperty="git.revision" failifexecutionfails="false" errorproperty="">
	        <arg value="describe"/>
	        <arg value="--tags"/>
	        <arg value="--always"/>
	        <arg value="HEAD"/>
	    </exec>
	    <condition property="repository.version" value="${git.revision}" else="unknown">
	        <and>
	            <isset property="git.revision"/>
	            <length string="${git.revision}" trim="yes" length="0" when="greater"/>
	        </and>
	    </condition>
	</target>

</project>