build.xml

<?xml version="1.0"?>
<!--
  ~ The MIT License
  ~
  ~ Copyright (c) 2016 Center for Bioinformatics, Peking University
  ~
  ~ Permission is hereby granted, free of charge, to any person obtaining a copy
  ~ of this software and associated documentation files (the "Software"), to deal
  ~ in the Software without restriction, including without limitation the rights
  ~ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
  ~ copies of the Software, and to permit persons to whom the Software is
  ~ furnished to do so, subject to the following conditions:
  ~
  ~ The above copyright notice and this permission notice shall be included in
  ~ all copies or substantial portions of the Software.
  ~
  ~ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
  ~ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
  ~ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
  ~ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
  ~ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
  ~ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
  ~ THE SOFTWARE.
  -->

<project name="MosaicHunter" default="onejar" basedir=".">

    <taskdef name="one-jar" classname="com.simontuffs.onejar.ant.OneJarTask"
         classpath="lib/one-jar-ant-task-0.97.jar" onerror="report"/>

    <property name="package" value="cn.edu.pku.cbi.mosaichunter" />
    <property name="packagedir" value="cn/edu/pku/cbi/mosaichunter" />
    <property name="jarfilename" value="mosaichunter.jar" />
    <property name="mainclass" value="${package}.MosaicHunter" />

    <!-- DIRECTORY SETUP -->
    <property name="srcdir" value="src" />
    <property name="libdir" value="lib/" />
    <property name="configdir" value="conf" />
    <property name="builddir" value="build" />
    <property name="build_classdir" value="${builddir}/classes" />

    <property environment="env"/>

    <property name="debug" value="off" />
    <property name="verbose" value="no" />

    <path id="classpath">
        <fileset dir="${libdir}">
          <include name="**/*.jar"/>
        </fileset>
    </path>

    <target name="compile" depends="clean">
        <mkdir dir="${build_classdir}"/>
        <javac srcdir="${srcdir}" destdir="${build_classdir}" includes="${packagedir}/**" debug="true" verbose="${verbose}" includeantruntime="false">
            <classpath refid="classpath" />
        </javac>
    </target>
    <target name="jar" depends="compile">
        <copy todir="${build_classdir}" overwrite="true"><fileset dir="${configdir}"/></copy>

        <pathconvert property="mf.classpath" pathsep=" ">
            <path refid="classpath" />
            <flattenmapper />
        </pathconvert>

        <jar jarfile="${builddir}/${jarfilename}" basedir="${build_classdir}">
            <manifest>
                <attribute name="Main-Class" value="${mainclass}"/>
                <attribute name="Class-Path" value="${mf.classpath} "/>
            </manifest>
        </jar>
    </target>
    <target name="onejar" depends="compile">
        <one-jar destfile="${builddir}/${jarfilename}">
            <manifest>
                <attribute name="One-Jar-Main-Class" value="${mainclass}"/>
            </manifest>
            <main>
                <fileset dir="${build_classdir}"/>
            	<fileset dir="${configdir}"/>            	                
            </main>
            <lib>
                <fileset dir="${libdir}" />
            </lib>
        </one-jar>
    </target>
    <target name="clean">
        <delete dir="${builddir}"/>
    </target>

</project>