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 -->
  <property name="build" location="build"/>
  <property name="dist" location="dist"/>
  <property name="lib"  location="lib"/>
  <property name="javadoc" location="javadoc" />

  <path id="thirdparty.dependencies">
    <fileset dir="${lib}" includes="*.jar" />
  </path>

  <path id="core.classpath">
    <path refid="thirdparty.dependencies" />
  </path>

  <path id="playground.classpath">
    <path refid="thirdparty.dependencies" />
    <fileset dir="${build}" includes="**/*.class" />
  </path>

  <path id="core.srcdir">
    <dirset dir="core/java/src"/>
  </path>

  <path id="playground.srcdir">
    <path refid="core.srcdir" />
    <dirset dir="playground/java/src" />
  </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="${target}.classpath"
           debug="true" debuglevel="lines,vars,source">
       <src refid="${target}.srcdir" />
    </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="org/broadinstitute/sting/utils/**" />
    </jar>

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

    <!-- Call special distribution methods for the playground.  Will not run if target isn't playground -->  
    <antcall target="dist.playground"/>

    <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="${dist}/FourBaseCaller.jar" basedir="${build}">
      <manifest>
        <attribute name="Class-Path" value="${jar.classpath}" />
        <attribute name="Main-Class" value="org.broadinstitute.sting.projects.fourbasecaller.FourBaseCaller" />
      </manifest>
    </jar>
  </target>

  <target name="dist.playground" if="target.is.playground">
    <jar jarfile="${dist}/Playground.jar">
      <fileset dir="${build}">
        <exclude name="org/broadinstitute/sting/utils/**" />
        <exclude name="org/broadinstitute/sting/gatk/**" />
      </fileset>
    </jar>

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

    <jar jarfile="${dist}/Playground.jar" update="true">
      <manifest>
        <attribute name="Class-Path" value="${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="${build}"/>
    <delete dir="${dist}"/>
    <delete dir="${lib}" />
  </target>
</project>