build.xml

<project name="gage" default="" basedir=".">
    <description>
        A build file for the GAGE code
    </description>
    <!-- Set global properties for this build -->
    <property file="build.properties"/>
    <property name="src.dir" location="./src"/>
    <property name="java.dir" location="./src/main/java"/>
    <property name="resources.dir" location="./src/main/resources"/>
    <property name="build.dir" location="./build"/>

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

    <target name="copy" depends="init">
        <!-- Copy source into build directory -->
        <copy todir="${build.dir}">
            <fileset dir="${src.dir}"/>
        </copy>

        <mkdir dir="${build.dir}/bin"/>
    </target>

    <target name="compile" depends="copy">
        <javac srcdir="${build.dir}/main/java"
               destdir="${build.dir}/bin"
               debug="on"/>
    </target>

    <target name="jar" depends="compile">
        <mkdir dir="${build.dir}/dist"/>
        <jar destfile="${build.dir}/dist/gage.jar" basedir="${build.dir}/bin"/>
    </target>

    <target name="test" depends="jar">
        <!-- Create test directory -->
        <mkdir dir="${build.dir}/test"/>
        <!-- Copy compiled java files into test directory -->
        <copy todir="${build.dir}/test">
            <fileset dir="${build.dir}/bin"/>
        </copy>
        <!-- Copy other files into test directory -->
        <copy todir="${build.dir}/test">
            <fileset dir="${build.dir}/main/resources"/>
        </copy>

        <!--
        <property environment="env"/>
        <exec dir="${build.dir}/test" executable="/bin/sh">
            <env key="PATH" path="${env.PATH}:${basedir}/build/test"/>
            <arg path="getCorrectnessStats.sh ../../test-data/aureus/genome.fasta ../../test-data/aureus/soapdenovo/genome.ctg.fasta ../../test-data/aureus/soapdenovo/genome.scf.fasta"/>
        </exec>
        -->
    </target>


    <target name="clean" description="clean up">
        <!-- Delete build directory -->
        <delete dir="${build.dir}"/>
    </target>

    <target name="purge" depends="clean"
            description="Removes build directory and galaxy source code">
        <delete dir="${build.dir}"/>
        <delete dir="${galaxy.src}"/>
    </target>


</project>