build.xml

<?xml version="1.0"?>
<project name="Macaw SNP typer" basedir="." default="dist">

	<property name="project" value="macaw" />

	<property name="manifest.mainClass" value="abeellab.macaw.MacawSNPtyper" />

	<fileset id="jarfiles" dir=".">

		<include name="lib/atk-*.jar" />

		<include name="lib/sam-*.jar" />

		<include name="lib/jannot-*.jar" />

		<include name="lib/ajt-*.jar" />

		<include name="lib_compile/scala-2.10.2/scala-library.jar" />
	</fileset>

	<!-- Code below should not be changed -->

	<property name="version" value="development" />

	<property name="src" value="src/" />

	<property name="build" value="build" />

	<property name="dist" value="${project}-${version}" />

	<property name="jar" value="${project}.jar" />

	<path id="build.classpath">

		<fileset refid="jarfiles" />
	</path>

	<echo message="${toString:build.classpath}" />

	<pathconvert pathsep=" " property="manifest.classpath">

		<path refid="build.classpath" />

		<mapper>

			<chainedmapper>

				<flattenmapper />

				<globmapper from="*.jar" to="*.jar" />
			</chainedmapper>
		</mapper>
	</pathconvert>

	<echo message="${manifest.classpath}" />

	<target name="dist">

		<!-- Define scala compiler task -->

		<taskdef resource="scala/tools/ant/antlib.xml">

			<classpath>

				<fileset refid="jarfiles" />

				<fileset dir="lib_compile">

					<include name="**/*.jar" />
				</fileset>
			</classpath>
		</taskdef>

		<delete dir="${build}" failonerror="false" />

		<delete dir="${dist}" failonerror="false" />

		<mkdir dir="${build}" />

		<mkdir dir="${dist}" />
		<mkdir dir="${dist}/${project}-${version}" />
		<copy todir="${dist}/${project}-${version}">
			 <fileset dir="lib/" >
                <include name="*.jar" />
            </fileset>
			<fileset dir="lib_compile/scala-2.10.2">
				<include name="scala-library.jar" />
			</fileset>
			<fileset dir="python">
				<include name="*.py" />
			</fileset>
		</copy>

		<propertyfile file="${build}/tool.properties">

			<entry key="program" value="${project}" />

			<entry key="version" value="${version}" />
		</propertyfile>

		<scalac destdir="${build}" excludes="junit/**" srcdir="${src}">

			<classpath path="${toString:build.classpath}">
			</classpath>
		</scalac>

		<javac debug="true" debuglevel="lines,vars,source" destdir="${build}" excludes="junit/*.java" source="1.6" srcdir="${src}" target="1.6">

			<classpath path="${toString:build.classpath}">
			</classpath>
		</javac>

		<copy todir="${build}/">

			<fileset dir="resources">

				<include name="*.txt" />

				
			</fileset>
			
		</copy>

		<jar basedir="${build}" destfile="${dist}/${project}-${version}/${jar}">

			<manifest>

				<attribute name="Main-Class" value="${manifest.mainClass}" />

				<attribute name="Class-Path" value="${manifest.classpath}" />
			</manifest>
		</jar>

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

		<delete dir="${dist}" failonerror="false" />

		<delete dir="${build}" failonerror="false" />
	</target>

</project>