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>

    <property name="source.dir" value="java/src" />
    <property name="single" value="*Test" />
    <property name="singleintegration" value="*IntegrationTest" />
    <property name="dist" value="dist" />

    <!-- should our junit test output go to a file or the screen?
    false means it goes to the screen (default) true to file -->
    <property name="usefile" value="false" />

    <!-- should our junit tests use XML? default is no -->
    <property name="testOutput" value="brief" />

    <!-- If running the 'package' task, this property controls the name of the xml file to package -->
    <property name="executable" value="GenomeAnalysisTK" />

    <!-- 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>

    <patternset id="dependency.mask" includes="*.jar">
        <exclude name="junit*.jar" />
        <exclude name="bcel*.jar" />
    </patternset>

    <path id="runtime.dependencies">
      <fileset dir="lib">
        <patternset refid="dependency.mask" />
      </fileset>
    </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"/>
    <property name="ivy.conf" value="default"/>
    <target name="resolve" depends="init"
            description="locate and download library dependencies">
      <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 file="ivy.xml" conf="${ivy.conf}" />
    </target>


    <!-- where to put reports and tests-->
    <property name="report" value="build/report"/>
    <property name="test.classes" value="build/testclasses"/>
    <property name="test.output" value="${dist}/test"/>
    <property name="test.sources" value="java/test"/>
    <property name="classes" value="classes"/>

    <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">
	<condition property="target.is.playground" value="true">
          <equals arg1="${target}" arg2="playground"/>
	</condition>
        
        <!-- Compile the java code from ${src} into build -->
        <javac srcdir="${source.dir}" destdir="build" debug="true" debuglevel="lines,vars,source" classpathref="runtime.dependencies">
            <!--compilerarg value="-Xlint:unchecked" /-->
             <exclude name="**/playground/**" unless="target.is.playground"/>
        </javac>
    </target>

    <target name="dist" depends="compile"
            description="generate the distribution">
        <mkdir dir="${dist}"/>
        <delete>
          <fileset dir="${dist}" includes="*.jar" />
        </delete>

        <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.CommandLineGATK"/>
            </manifest>
        </jar>

        <jar jarfile="${dist}/FourBaseRecaller.jar" whenmanifestonly="skip">
          <fileset dir="build">
            <include name="**/secondarybase/**/*.class" />
          </fileset>
          <manifest>
            <attribute name="Main-Class" value="org.broadinstitute.sting.secondarybase.FourBaseRecaller" />
          </manifest>
        </jar>
    
        <jar jarfile="${dist}/Playground.jar" whenmanifestonly="skip">
            <fileset dir="build">
                <include name="**/*.class"/>
                <exclude name="**/utils/**"/>
                <exclude name="**/gatk/**"/>
                <exclude name="**/secondarybase/**" />
            </fileset>
        </jar>

        <pathconvert property="jar.classpath" pathsep=" ">
            <flattenmapper/>
            <fileset dir="${dist}" includes="*.jar"/>
            <filelist files="GATKScala.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="${dist}/FourBaseRecaller.jar" update="true" whenmanifestonly="skip">
            <manifest>
                <attribute name="Class-Path" value="${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="core" description="force a build of the Sting core code">
        <antcall target="dist" inheritAll="true">
            <param name="target" value="core" />
        </antcall>
    </target>

    <target name="playground" description="force a build of the Sting experimental code">
        <antcall target="dist" inheritAll="true">
            <param name="target" value="playground" />
	</antcall>
    </target>

    <target name="test.compile" depends="playground">
        <echo message="Sting: Compiling test cases!"/>
        <mkdir dir="${test.classes}"/>
        <javac destdir="${test.classes}" debug="true" optimize="on">
            <src path="${test.sources}"/>
            <classpath>
                <path refid="runtime.dependencies" />
                <pathelement location="build"/>
                <pathelement location="lib/junit-4.4.jar"/>
            </classpath>
        </javac>
    </target>

    <!-- new scala target -->
    
    <target name="scala" description="build the scala directory">
      <antcall target="resolve">
        <param name="ivy.conf" value="scala"/>
      </antcall>
        <antcall target="dist"/>    
      <property name="scala.src" value="scala/src" />
      <property name="scala.classes" value="scala/classes" />
      <pathconvert property="scalajar.classpath" pathsep=";">
        <flattenmapper/>
        <fileset dir="${basedir}" includes="dist/*.jar"/>
      </pathconvert>
      
      <path id="scala.classpath">
        <pathelement location="lib/scala-compiler-2.7.7.jar"/>
        <pathelement location="lib/scala-library-2.7.7.jar"/>
        <fileset dir="${dist}">
          <patternset id="scalaStuff">
            <include name="*.jar"/>
        </patternset>
        </fileset>
      </path>
      <taskdef resource="scala/tools/ant/antlib.xml">
        <classpath refid="scala.classpath"/>
      </taskdef>
      <mkdir dir="${scala.classes}"/>
      <echo>Building Scala...</echo>
      <scalac srcdir="${scala.src}" destdir="${scala.classes}" classpathref="scala.classpath" force="changed">
        <include name="**/*.scala"/>
      </scalac>
      
      <jar jarfile="${dist}/GATKScala.jar">
        <fileset dir="${scala.classes}">
          <include name="**/*.class"/>
        </fileset>
      </jar>
    </target>
    



    <!-- TEST -->
    <target name="test" depends="test.compile,agent" description="Run unit tests">
        <mkdir dir="${report}"/>
        <echo message="Sting: Running test cases!"/>
        <junit printsummary="yes" showoutput="yes" clonevm="yes" haltonfailure="yes" failureProperty="test.failure">
            <jvmarg value="-javaagent:build/TestAgent.jar"/>
            <formatter type="${testOutput}" usefile="${usefile}" />
            <classpath>
                <path refid="runtime.dependencies"/>
                <pathelement location="build"/>
                <pathelement location="${test.classes}"/>
                <pathelement location="lib/junit-4.4.jar"/>
            </classpath>

            <batchtest fork="yes" todir="${report}">
                <fileset dir="${test.classes}">
                    <include name="**/${single}.class"/>
                    <exclude name="**/BaseTest.class"/>
                    <exclude name="**/*IntegrationTest.class"/>
                </fileset>
            </batchtest>
        </junit>
        <fail message="test failed" if="test.failure" />
    </target>
    <!-- Our long tests, tests that are more software integration and test -->
    <target name="integrationtest" depends="test.compile"
            description="Run the long integration unit tests">
        <mkdir dir="${report}"/>
        <echo message="Sting: Running integration test cases!"/>
        <junit printsummary="yes" showoutput="yes" clonevm="yes" haltonfailure="yes" failureProperty="test.failure">

            <jvmarg value="-Xdebug"/>
            <jvmarg value="-Xrunjdwp:transport=dt_socket,server=y,suspend=n,address=8090"/>
            <formatter type="${testOutput}" usefile="${usefile}" />
            <classpath>
                <path refid="runtime.dependencies"/>
                <pathelement location="${dist}/GenomeAnalysisTK.jar"/>
                <pathelement location="${test.classes}"/>
                <pathelement location="lib/junit-4.4.jar"/>
            </classpath>

            <batchtest fork="yes" todir="${report}">
                <fileset dir="${test.classes}">
                  <include name="**/${singleintegration}.class"/>
                </fileset>
            </batchtest>
        </junit>
        <fail message="test failed" if="test.failure" />
    </target>

    <!-- this builds the instrumentation library we're going to use for test cases -->
    <target name="agent" description="build the agent">
        <echo message="Sting: Creating test agent!"/>
        <jar jarfile="build/TestAgent.jar">
            <fileset dir="build">
            <include name="**/TrivialInstrumenter.class" />
          </fileset>

            <manifest>
                <attribute name="Class-Path" value="${jar.classpath}"/>
                <attribute name="Premain-Class" value="org.broadinstitute.sting.TrivialInstrumenter"/>
            </manifest>
        </jar>
    </target>
    
    <target name="javadoc" depends="init,resolve" description="generates javadoc">
        <mkdir dir="javadoc"/>
	<!-- Javadoc can't take the same dirsets as javac; it only likes getting the base directory -->
	<!-- Exclude playground files with excludepackagenames instead of the "source" dirset -->
    	<condition property="package.excludes" value="" else="org.broadinstitute.sting.playground.*">
              <equals arg1="${target}" arg2="playground" />
	    </condition>
        <javadoc destdir="javadoc" sourcepath="${source.dir}" excludepackagenames="${package.excludes}" classpathref="runtime.dependencies"/>
    </target>

    <!-- Unzip all classes from their current locations and assemble them in a staging directory -->
    <target name="stage" description="stage files for distribution">
        <mkdir dir="staging"/>
        <unjar dest="staging" overwrite="false">
          <fileset dir="${dist}">
            <patternset refid="dependency.mask" />
          </fileset>
        </unjar>
    </target>

    <!-- Build a package consisting of all supporting files -->
    <target name="package" depends="dist,stage" description="bundle up an executable for distribution">
        <mkdir dir="${dist}/packages" />
        <xslt in="packages/${executable}.xml" out="${dist}/packages/Build${executable}.xml" style="packages/CreatePackager.xsl" />
        <ant antfile="${dist}/packages/Build${executable}.xml" />
    </target>

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