build.xml

<project name="TASSEL" default="dist" basedir=".">
    
    <description>
        TASSEL: Trait Analysis by a SSociation, Evolution and Linkage
        The TASSEL project (http://www.maizegenetics.net) may be distributed
        under the terms of the GNU Lesser General Public License
    </description>
    
    <!-- set global properties for this build -->
    <property name="src" location="src"/>
    <property name="build" location="build"/>
    <property name="dist" location="dist"/>
    <property name="lib" location="lib"/>
    <property name="lib_deploy" location="..\lib_deploy"/>
    <property name="images_plugins" value="net\maizegenetics\baseplugins\images"/>
    <property name="images" value="net\maizegenetics\tassel\images"/>
    
    <property name="tassel" location="${dist}\sTASSEL.jar"/>
    <property name="tasselGBS" location="${dist}\sTASSELGBS.jar"/>
    <property name="test" location="test"/>
    <property name="pal_src" value="${basedir}/src/net/maizegenetics/pal"/>
    <property name="keystore_dir" value="${basedir}/common"/>
    <property name="javadoc" value="${basedir}/javadoc"/>
    
    
    <path id="build.class.path">
        <fileset dir="${lib}">
            <include name="*.jar"/>
            <include name="*.zip"/>
        </fileset>
    </path>

    <pathconvert property="manifest.classpath" pathsep=" ">
        <path refid="build.class.path"/>
        <mapper>
            <chainedmapper>
                <flattenmapper/>
                <globmapper from="*.jar" to="lib/*.jar"/>
            </chainedmapper>
        </mapper>
    </pathconvert>
    
    
    <target name="init">
        
        <!-- Create the time stamp -->
        <tstamp>
            <format property="" pattern=""/>
        </tstamp>
        
        <!-- Create the build directory structure used by compile -->
        <mkdir dir="${build}"/>
        <mkdir dir="${dist}"/>
        
    </target>
    
    
    <target name="genome" depends="init" description="compile the source">
        <javac compiler="javac1.8" target="1.8" includeantruntime="false" srcdir="${src}" destdir="${build}" debug="true">
            <include name="net/maizegenetics/genome/**"/>
            <include name="net/maizegenetics/gbs/**"/>
            <include name="net/maizegenetics/gwas/**"/>
            <classpath>
                <pathelement path="${lib}"/>
                <fileset dir="${lib}">
                    <include name="**/*.jar"/>
                </fileset>
            </classpath>
        </javac>
    </target>
    
    <target name="compile" depends="init" description="compile the source">
        <!-- Compile the java code from ${src} into ${build} -->
        <javac compiler="javac1.8" target="1.8" includeantruntime="false" srcdir="${src}" destdir="${build}" debug="true">
            <exclude name="**/Test*"/>
            <exclude name="net/maizegenetics/genome/**"/>
            <exclude name="net/maizegenetics/gbs/**"/>
            <exclude name="net/maizegenetics/gwas/**"/>
            <classpath>
                <pathelement path="${lib}"/>
                <fileset dir="${lib}">
                    <include name="**/*.jar"/>
                    <include name="**/*.zip"/>
                </fileset>
            </classpath>
        </javac>
    </target>
    
    <target name="dist" depends="clean, compile" description="distribution">
        
        <!-- Create the distribution directory -->
        <mkdir dir="${dist}"/>
        
        <copy todir="${build}" description="copy images">
            <fileset dir="${src}">
                <include name="**/*.gif"/>
                <include name="**/*.GIF"/>
                <include name="**/*.html"/>
            </fileset>
        </copy>
        
        <jar jarfile="${tassel}" basedir="${build}">
            <manifest>
                <attribute name="Built-By" value="${user.name}"/>
                <attribute name="Main-Class" value="net.maizegenetics.tassel.TASSELMainApp"/>
                <attribute name="Class-Path" value="${manifest.classpath}"/>
            </manifest>
        </jar>
        
        <signjar jar="${tassel}" alias="http://www.maizegenetics.net/tassel" storepass="EdBuckler" keystore="${keystore_dir}/keystore"/>
        
    </target>
    
    <target name="distGBS" depends="clean, compile, genome" description="distribution">
        
        <!-- Create the distribution directory -->
        <mkdir dir="${dist}"/>
        
        <copy todir="${build}" description="copy images">
            <fileset dir="${src}">
                <include name="**/*.gif"/>
                <include name="**/*.GIF"/>
                <include name="**/*.html"/>
            </fileset>
        </copy>
        
        <jar jarfile="${tasselGBS}" basedir="${build}">
            <manifest>
                <attribute name="Built-By" value="${user.name}"/>
                <attribute name="Main-Class" value="net.maizegenetics.tassel.TASSELMainApp"/>
                <attribute name="Class-Path" value="${manifest.classpath}"/>
            </manifest>
        </jar>
        
        <signjar jar="${tasselGBS}" alias="http://www.maizegenetics.net/tassel" storepass="EdBuckler" keystore="${keystore_dir}/keystore"/>
        
    </target>
    
    
    <target name="javadoc">
        
        <delete dir="${javadoc}"/>
        <mkdir dir="${javadoc}"/>
        
        <javadoc packagenames="net.*"
                 source="1.8"
                 destdir="${javadoc}"
                 author="true"
                 use="true"
                 windowtitle="net.maizegenetics API"
                 doctitle="TASSEL: Trait Analysis by aSSociation, Evolution and Linkage">
            <classpath refid="build.class.path"/>
            
            <sourcepath>
                <pathelement path="${basedir}/src"/>
            </sourcepath>
        </javadoc>
        
    </target>
    
    
    <target name="run" description="Run the program">
        <copy file="${tassel}" todir="${test}"/>
        <copy file="${lib}\gdpc.jar" todir="${test}" />
        <copy file="${lib_deploy}\tasselLib.zip" todir="${test}" />
        <!-- run the class -->
        <java classname="net.maizegenetics.tassel.TASSELMainApp" fork="true" spawn="true">
            <arg value="-h"/>
            <jvmarg value="-Xms128m"/>
            <jvmarg value="-Xmx256m"/>
            <classpath>
                <!-- include all jar files  -->
                <pathelement location="${test}/tasselLib.zip"/>
                <pathelement location="${test}/sTASSEL.jar"/>
                <pathelement location="${test}/browser.jar"/>
            </classpath>
        </java>
    </target>
    
    <target name="clean" description="clean up">
        <delete dir="${build}"/>
    </target>
    
</project>