build.xml

<project name="PEPR" default="dist" basedir=".">
    <description>
        simple example build file
    </description>
  <!-- set global properties for this build -->
  <property name="src" location="src"/>
  <property name="build" location="build"/>
  <property name="dist"  location="dist"/>
  <property name="bin"  location="pepr-bin"/>
  <property name="lib"  location="lib"/>
  <property name="scripts"  location="scripts"/>
  
  <path id="project.classpath">
          <fileset dir="lib" includes="*.jar" />
  </path>

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

  <target name="compile" depends="init"
        description="compile the source " >
    <!-- Compile the java code from ${src} into ${build} -->
    <javac debug="true" srcdir="${src}" classpathref="project.classpath" destdir="${build}"/>
  </target>

  <target name="dist" depends="compile"
        description="generate the distribution" >
    <!-- Create the distribution directory -->
    <mkdir dir="${dist}/pepr/lib"/>

  	<!-- unzip any jar files in the lib directory, and put the contents in  -->
    <!-- the build directory so they will be packed into the distribution jar file-->

  	<unzip dest="${build}">
        <fileset dir="lib" includes="*.jar" />
    </unzip>

  	<copy file="BLOSUM62" todir="${build}"/>

    <!-- Put everything in ${build} into the pepr.jar file -->
    <jar jarfile="${dist}/pepr/lib/pepr.jar" basedir="${build}"/>

  	<!-- copy everything to dist directory for tar -->
 <!--
  	<copy todir="${dist}/pepr/bin_mac">
      <fileset dir="${bin}_mac"/>
    </copy>
 -->
  	<exec executable="cp">
  	    <arg line="-R ${bin}_mac ${dist}/pepr/bin_mac"/>
  	</exec>
  	
  	<exec executable="cp">
  	    <arg line="-R ${bin}_linux ${dist}/pepr/bin"/>
  	</exec>
  	
<!--  	
    <copy todir="${dist}/pepr/bin">
      <fileset dir="${bin}_linux"/>
    </copy>
-->
  	
    <copy todir="${dist}/pepr/lib">
      <fileset dir="${lib}"/>
    </copy>
    
    <copy todir="${dist}/pepr/scripts">
      <fileset dir="${scripts}"/>
    </copy>
    
    <tar compression="gzip" destfile="pepr-${DSTAMP}.tar" basedir="${dist}"/>
    
    </target>

  <target name="clean"
        description="clean up" >
    <!-- Delete the ${build} and ${dist} directory trees -->
    <delete dir="${build}"/>
    <delete dir="${dist}"/>
  </target>
</project>