build.xml

<project name="fastqc" default="dist" basedir=".">
    <description>
        builds fastqc with filtering for reads in bam file .
        build file is not done.
        currently simply copying the class folders etc.. to deploy
    </description>
    <!-- set global properties for this build -->
    <property name="src" location="uk"/>
    <property name="build" location="build"/>
    <property name="dist"  location="dist"/>
    <property name="deploy"  location="fastqc-csf"/>

    <target name="init">
        <!-- Create the time stamp -->
        <tstamp/>
        <!-- Create the build directory structure used by compile -->
        <mkdir dir="${build}"/>
    </target>

    <target name="compile" depends="init"
            description="compile the source " >
        <!-- Compile the java code from ${src} into ${build} -->
        <javac srcdir="${src}" destdir="${build}">
            <classpath>
                <fileset dir=".">
                    <include name="**/*.jar" />
                </fileset>
            </classpath>
        </javac>
    </target>

    <target name="dist" depends="compile"
            description="generate the distribution" >
        <!-- Create the distribution directory -->
        <mkdir dir="${dist}"/>

        <!-- Put everything in ${build} into the MyProject-${DSTAMP}.jar file -->
        <jar jarfile="${dist}/fastqc.jar" basedir="${build}"/>
    </target>

    <target name="deploy" depends="clean,compile"
            description="generate the distribution as as simple folder like original fastqc" >
        <!-- Create the distribution directory -->
        <mkdir dir="${deploy}"/>
        <copy todir="${deploy}">
            <fileset dir="${build}"/>
	    <fileset dir="../FastQC" excludes="uk/**,out/**,lib/**,build/**"/>
        </copy>

        <!-- Put everything in ${build} into the MyProject-${DSTAMP}.jar file -->

    </target>

    <target name="clean"
            description="clean up" >
        <!-- Delete the ${build} and ${dist} directory trees -->
        <delete dir="${build}"/>
        <delete dir="${dist}"/>
        <delete dir="${deploy}"/>
    </target>
</project>