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>


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


    <!-- TEST -->
    <target name="test" depends="test.compile">
        <mkdir dir="${report}"/>
        <echo message="Sting: Running test cases!"/>
        <junit printsummary="yes" clonevm="yes" haltonfailure="yes">
            <formatter type="plain"/>
            
            <classpath>
                <path refid="thirdparty.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="**/*.class"/>
                </fileset>
            </batchtest>
        </junit>

    </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">
            <!--compilerarg value="-Xlint:unchecked" /-->
            <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" description="generates javadoc">
        <mkdir dir="javadoc"/>
        <javadoc sourcepathref="source" destdir="javadoc"/>
    </target>

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