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" />

    <!-- 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>

    <path id="external.dependencies">
        <fileset dir="lib" includes="*.jar"/>
    </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>


    <!-- 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" classpathref="external.dependencies"
               debug="true" debuglevel="lines,vars,source">
            <!--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/SomaticCoverage.jar" whenmanifestonly="skip">
          <fileset dir="build">
            <include name="**/somaticcoverage/*.class"/>
            <include name="**/walkers/SomaticCoverageWalker.class"/>
            
          </fileset>
          <fileset dir="java">
            <include name="**/somaticcoverage/*.xml"/>
          </fileset>
            <manifest>
            <attribute name="Main-Class" value="org.broadinstitute.sting.playground.somaticcoverage.SomaticCoverageTool" />
          </manifest>
        </jar>


        <jar jarfile="dist/AnnotateSecondaryBase.jar" whenmanifestonly="skip">
          <fileset dir="build">
            <include name="**/secondarybase/**/*.class" />
          </fileset>
          <manifest>
            <attribute name="Main-Class" value="org.broadinstitute.sting.secondarybase.AnnotateSecondaryBase" />
          </manifest>
        </jar>

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

        <jar jarfile="dist/MatchSQTagToStrand.jar" whenmanifestonly="skip">
          <fileset dir="build">
            <include name="**/secondarybase/**/*.class" />
          </fileset>
          <manifest>
            <attribute name="Main-Class" value="org.broadinstitute.sting.secondarybase.MatchSQTagToStrand" />
          </manifest>
        </jar>

        <jar jarfile="dist/AddFourProbsToSAM.jar" whenmanifestonly="skip">
          <fileset dir="build">
            <include name="**/secondarybase/**/*.class" />
          </fileset>
          <manifest>
            <attribute name="Main-Class" value="org.broadinstitute.sting.secondarybase.AddFourProbsToSAM" />
          </manifest>
        </jar>
-->

        <jar jarfile="dist/Playground.jar" whenmanifestonly="skip">
            <fileset dir="build">
                <include name="**/*.class"/>
                <exclude name="**/utils/**"/>
                <exclude name="**/gatk/**"/>
            </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/FourBaseRecaller.jar" update="true" whenmanifestonly="skip">
            <manifest>
                <attribute name="Class-Path" value="${jar.classpath}" />
            </manifest>
        </jar>

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

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

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

        <jar jarfile="dist/AddFourProbsToSAM.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>
        
        <jar jarfile="dist/SomaticCoverage.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="compile">
        <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="external.dependencies"/>
                <pathelement location="build"/>
                <pathelement location="lib/junit-4.4.jar"/>
            </classpath>
        </javac>
    </target>

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

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