build.xml

<project name="Berkeley Aligner" default="distribute-clean" basedir=".">

	<property name="src" value="./src/" />
	<property name="build.dir" value="./classes/" />

	<property name="dist.dir" value="./distribution/" />
	<property name="jarfile" value="berkeleyaligner.jar" />

	<property name="manifest" value="./resources/Manifest.mf" />
	<property name="dist.readme" value="./resources/distribution_readme.txt" />
	<property name="dist.conf" value="./resources/example_conf.txt" />
	<property name="dist.syntactic.conf" value="./resources/example_syntactic_conf.txt" />
	<property name="dist.runscript" value="./resources/run_script.sh" />

	<property name="example.dir" value="./resources/example/" />
	<property name="dist.example.dir" value="${dist.dir}/example/" />
	<property name="doc.dir" value="./documentation/" />
	<property name="dist.doc.dir" value="${dist.dir}/documentation/" />

	<property name="distfile" value="./berkeleyaligner" />
	<property name="tarfile" value="${distfile}.tar" />
	<property name="gzipfile" value="${tarfile}.gz" />

	<property name="srcfile" value="${distfile}-src" />
	<property name="srctarfile" value="${srcfile}.tar" />
	<property name="srcgzipfile" value="${srctarfile}.gz" />

	<target name="distribute-clean" depends="clean, distribute" />

	<target name="package-source" depends="clean">
		<tar destfile="${srcgzipfile}" compression="gzip">
			<tarfileset prefix="berkeleyaligner" dir="${basedir}" excludes="private/**"/>
		</tar>
	</target>

	<target name="init-distribute">
		<mkdir dir="${dist.dir}" />
		<mkdir dir="${dist.example.dir}" />
		<mkdir dir="${dist.doc.dir}" />
	</target>

	<target name="distribute" depends="compile, init-distribute">
		<jar destfile="${dist.dir}/${jarfile}" basedir="${build.dir}" manifest="${manifest}" />

		<copy todir="${dist.example.dir}" overwrite="false">
			<fileset dir="${example.dir}" />
		</copy>
		<copy todir="${dist.doc.dir}" overwrite="false">
			<fileset dir="${doc.dir}" />
		</copy>

		<copy file="${dist.readme}" tofile="${dist.dir}/README" overwrite="false" />
		<copy file="${dist.conf}" tofile="${dist.dir}/example.conf" overwrite="false" />
		<copy file="${dist.syntactic.conf}" tofile="${dist.dir}/example_syntactic.conf" overwrite="false" />
		<copy file="${dist.runscript}" tofile="${dist.dir}/align" overwrite="false" />
		<chmod file="${dist.dir}/align" perm="755" />

		<tar destfile="${gzipfile}" compression="gzip">
			<tarfileset prefix="berkeleyaligner" dir="${dist.dir}" />
		</tar>
	</target>

	<target name="compile">
		<mkdir dir="${build.dir}" />
		<javac srcdir="${src}" destdir="${build.dir}" optimize="on" debug="on">
			<classpath>
				<pathelement location="${build.dir}" />
			</classpath>
		</javac>
	</target>

	<target name="clean">
		<delete dir="${build.dir}" />
		<delete dir="${dist.dir}" />
		<delete file="${gzipfile}" />
	</target>

</project>