gatk-3.8/java/build.xml

<project name="AnalysisTK" default="dist" basedir="." xmlns:ivy="antlib:org.apache.ivy.ant">
    <description>
        simple 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="lib"  location="lib"/>

  <!-- ivy properties -->
  <property name="ivy.install.version" value="2.0.0" />
  <property name="ivy.home" value="${user.home}/.ant" />
  <property name="ivy.jar.dir" value="${ivy.home}/lib" />
  <property name="ivy.jar.file" value="ivy-${ivy.install.version}.jar" />
  <property name="ivy.settings.dir" value="settings" />
  <property file="${ivy.settings.dir}/ivysettings.properties" />

  <target name="resolve">
    <mkdir dir="${ivy.jar.dir}" />
    <get src="http://repo1.maven.org/maven2/org/apache/ivy/ivy/${ivy.install.version}/${ivy.jar.file}"
         dest="${ivy.jar.dir}/${ivy.jar.file}" 
         usetimestamp="true"/>
    <taskdef resource="org/apache/ivy/ant/antlib.xml" 
             uri="antlib:org.apache.ivy.ant" 
             classpath="${ivy.jar.dir}/${ivy.jar.file}" />
    <ivy:settings file="${ivy.settings.dir}/ivysettings.xml" />
    <ivy:retrieve />
  </target>

  <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,resolve"
        description="compile the source " >
    <!-- Compile the java code from ${src} into ${build} -->
    <javac srcdir="${src}" destdir="${build}" >
      <classpath>
        <fileset dir="lib">
          <include name="*.jar" />
        </fileset>
      </classpath>
    </javac>
  </target>

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

    <!-- Put everything in ${build} into the MyProject-${DSTAMP}.jar file -->
    <jar jarfile="${dist}/AnalysisTK.jar" basedir="${build}">
      <manifest>
        <attribute name="Class-Path" value="functionalj-1.0.jar picard-snapshot.jar sam-1.0.jar" />
        <attribute name="Main-Class" value="edu.mit.broad.sting.atk.AnalysisTK" />
      </manifest>
    </jar>

    <copy todir="${dist}">
      <fileset dir="${lib}" includes="*.jar" />
    </copy>
  </target>

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