build.xml

<project name="MBSV" default="distCode" basedir=".">
    <description>
        Build jar file for MBSV code
    </description>
  <!-- set global properties for this build -->

  <property name="srcMBSV" location="src"/>
  <property name="buildMBSV" location="build"/>
  <property name="libMBSV" location="lib"/>
  <property name="binMBSV" location="bin"/>
  

  <target name="clean"
       description="clean up" >
    <!-- Delete the ${build} directory tree -->
    <delete dir="${buildMBSV}"/>
    <delete dir="${libMBSV}"/> 
    <delete dir="${binMBSV}"/> 
  </target>

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

  <target name="compileMBSV" depends="init"
        description="compile the source " >

    <!-- Compile the java code from ${srcMBSV} into ${buildMBSV} -->
    <javac srcdir="${srcMBSV}" includeantruntime="false" destdir="${buildMBSV}"/>

    <!-- Compile cython from ${srcMBSV} into ${buildMBSV} -->
    <exec executable="python" failonerror="true">
      <arg line="setup.py"/>
      <arg line="build_ext"/>
      <arg line="--build-lib=${libMBSV}/"/>
      <arg line="--build-temp=${buildMBSV}/"/>
    </exec>

  </target>

  <target name="distMBSV" depends="compileMBSV"
	  description="generate the distribution MultiBreakSV.jar" >

	<!-- make jar file for MBSV -->
	<jar jarfile="${binMBSV}/MultiBreakSV.jar" basedir="${buildMBSV}">
		<manifest>
			<attribute name="Main-Class" value="MultiBreakSV"/>
		</manifest>
	</jar>

	<!-- make jar file for external sort -->
	<jar jarfile="${libMBSV}/ExternalSort.jar" basedir="${buildMBSV}">
		<manifest>
			<attribute name="Main-Class" value="GeneralExternalSort"/>
		</manifest>
	</jar>

	<!-- copy python and perl files to bin and lib dirs -->
	<copy file="${srcMBSV}/M5toMBSV.py" todir="${binMBSV}/"/>
	<copy file="${srcMBSV}/generateIndependentSubproblems.pl" todir="${binMBSV}/"/>
	<copy file="${srcMBSV}/constructMultiBreakpointAlignments.pl" todir="${libMBSV}/"/>
	<copy file="${srcMBSV}/parseRm5ForDeletionsCython.py" todir="${libMBSV}/"/>
	<copy file="${srcMBSV}/quick-post-process.py" todir="${binMBSV}/"/>

  </target>

  <target name="distCode" depends="distMBSV"
        description="generates source code" >
  </target>

</project>