gatk-3.8/build.xml

<project name="Sting" default="dist" basedir="." xmlns:ivy="antlib:org.apache.ivy.ant">
  <description>Compile and distribute the Sting toolkit</description>

  <!-- Set target based on STING_BUILD_TYPE environment variable -->
  <property environment="env" />
  <condition property="target" value="playground" else="core">
    <equals arg1="${env.STING_BUILD_TYPE}" arg2="playground" casesensitive="false" />
  </condition>
  <condition property="target.is.playground" value="true">
    <equals arg1="${target}" arg2="playground" />
  </condition>

  <!-- set global properties for this build -->
  <path id="thirdparty.dependencies">
    <fileset dir="lib" includes="*.jar" />
  </path>

  <path id="source">
    <dirset dir="java/src">
      <patternset>
        <include name="org/broadinstitute/sting/*" />
        <exclude name="**/playground/**" unless="target.is.playground" />
      </patternset>
    </dirset>
  </path>

  <!-- 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" depends="init"
          description="locate and download library dependencies">
    <!-- retrieve ivy if necessary -->
    <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}/${ivy.jar.file}" 
         usetimestamp="true"/>
    <!-- initialize and load ivy -->
    <taskdef resource="org/apache/ivy/ant/antlib.xml" 
             uri="antlib:org.apache.ivy.ant" 
             classpath="${ivy.jar.dir}/${ivy.jar.file}" />
    <ivy:settings file="${ivy.settings.dir}/ivysettings.xml" />
    <!-- retrieve dependencies -->
    <ivy:retrieve />
  </target>

  <target name="init">
    <!-- Create the time stamp -->
    <tstamp/>

    <echo message="Compiling module ${target}" />

    <!-- 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 destdir="build" classpathref="thirdparty.dependencies"
           debug="true" debuglevel="lines,vars,source">
       <src refid="source" />
    </javac>
  </target>

  <target name="dist" depends="compile"
          description="generate the distribution" >
    <mkdir dir="dist"/>

    <copy todir="dist">
      <fileset dir="lib" includes="*.jar" />
    </copy>

    <jar jarfile="dist/StingUtils.jar">
      <fileset dir="build" includes="**/utils/**/*.class" />
    </jar>

    <jar jarfile="dist/GenomeAnalysisTK.jar">
      <fileset dir="build" includes="**/gatk/**/*.class" />
      <manifest>
        <attribute name="Main-Class" value="org.broadinstitute.sting.gatk.GenomeAnalysisTK" />
      </manifest>
    </jar>

    <jar jarfile="dist/FourBaseCaller.jar" whenmanifestonly="skip">
      <fileset dir="build" includes="**/fourbasecaller/**/*.class" />
      <manifest>
        <attribute name="Main-Class" value="org.broadinstitute.sting.playground.fourbasecaller.FourBaseCaller" />
      </manifest>
    </jar>

    <jar jarfile="dist/FourBaseRecaller.jar" whenmanifestonly="skip">
      <!--<fileset dir="build" includes="**/fourbasecaller/**/*.class" />-->
      <fileset dir="build">
        <include name="**/fourbasecaller/**/*.class" />
        <include name="**/illumina/**/*.class" />
      </fileset>
      <manifest>
        <attribute name="Main-Class" value="org.broadinstitute.sting.playground.fourbasecaller.FourBaseRecaller" />
      </manifest>
    </jar>

    <jar jarfile="dist/Playground.jar" whenmanifestonly="skip">
      <fileset dir="build">
        <include name="**/*.class" />
        <exclude name="**/utils/**" />
        <exclude name="**/gatk/**" />
        <exclude name="**/fourbasecaller/**" />
      </fileset>
    </jar>

    <pathconvert property="jar.classpath" pathsep=" ">
      <flattenmapper />
      <fileset dir="dist" includes="*.jar" />
    </pathconvert>

    <jar jarfile="dist/StingUtils.jar" update="true">
      <manifest>
        <attribute name="Class-Path" value="${jar.classpath}" />
      </manifest>
    </jar>

    <jar jarfile="dist/GenomeAnalysisTK.jar" update="true">
      <manifest>
        <attribute name="Class-Path" value="${jar.classpath}" />
      </manifest>
    </jar>

    <jar jarfile="dist/FourBaseCaller.jar" update="true" whenmanifestonly="skip">
      <manifest>
        <attribute name="Class-Path" value="${jar.classpath}" />
      </manifest>
    </jar>

    <jar jarfile="dist/FourBaseRecaller.jar" update="true" whenmanifestonly="skip">
      <manifest>
        <attribute name="Class-Path" value="${jar.classpath}" />
      </manifest>
    </jar>

    <jar jarfile="dist/Playground.jar" update="true" whenmanifestonly="skip">
      <manifest>
        <attribute name="Class-Path" value="${jar.classpath}" />
      </manifest>
    </jar>
  </target>

  <target name="javadoc">
    <mkdir dir="javadoc" />
    <javadoc sourcepathref="${target}.srcdir" destdir="javadoc" />
  </target>

  <target name="clean"
          description="clean up" >
    <delete dir="out" />
    <delete dir="build" />
    <delete dir="dist" />
    <delete dir="lib" />
  </target>
</project>