build.xml

<!-- 
 *****************************************************************************
 *                                                                           *
 *   PLAST : Parallel Local Alignment Search Tool                            *
 *   Copyright (c) 2015 Inria                                                *
 *                                                                           *
 *   PLAST is free software; you can redistribute it and/or modify it under  *
 *   the Affero GPL v3 License                                               *
 *                                                                           *
 *   This program is distributed in the hope that it will be useful,         *
 *   but WITHOUT ANY WARRANTY; without even the implied warranty of          *
 *   MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the            *
 *   Affero GPL v3 License for more details.                                 *
 *****************************************************************************

    Ant project file to handle PLAST java exemple. 
    
    Requirements: Oracle Java JDK 1.7 or above, Apache Ant 1.9.1 or above.
    
    
    author: Patrick Durand, Inria
    date: Nov. 18, 2015

-->
<project name="plast" 
         basedir="." 
         default="help" 
         xmlns:unless="ant:unless">

    <!-- some properties -->
    <property name="src.dir"     value="src"/>
    <property name="build.dir"   value="build"/>
    <property name="pack.dir"    value="${basedir}/package/plast-java"/>
    <property name="classes.dir" value="${build.dir}/classes"/>
    <property name="jar.dir"     value="${basedir}/thirdparty"/>

	<!-- check ant and java version -->
    <target name="checkversion">
        <echo>Current Ant version is: ${ant.version}</echo>
        <fail message="***   Ant 1.9.1+ required   ***">
          <!-- ant 1.9.1 introduced unless directive used in this script-->
          <condition>
           <not><antversion atleast="1.9.1" /></not>
          </condition>
        </fail>
        <echo>  ok</echo>
        <echo>Current Java version is: ${ant.java.version}</echo>
        <fail message="***   Oracle Java SDK 1.7+ not found   ***">
		  <condition>
	  		<not>
	  		  <or>   
	   		    <equals arg1="1.7" arg2="${ant.java.version}"/>
	   		    <equals arg1="1.8" arg2="${ant.java.version}"/>
			    <equals arg1="1.9" arg2="${ant.java.version}"/>
		      </or>
		    </not>   
		</condition>
        </fail>
        <echo>  ok</echo>
    </target>
	
	<!-- delete build directory -->
    <target name="clean">
        <delete dir="${build.dir}"/>
    </target>

	<!-- compile source code -->
    <target name="compile" depends="checkversion,clean">
        <mkdir dir="${classes.dir}"/>
        <javac 
          		classpath="${jar.dir}/plast.jar"
          		destdir="${classes.dir}"
        		compiler="javac1.7"
        		includeAntRuntime="false">
    	  <src path="${src.dir}"/>
    	</javac>
    </target>

    <!-- first main target: clean build directory and run a fresh source code compiling -->
    <target name="cmp" depends="checkversion,clean,compile"/>

    <!-- second main target: run the software -->
	<target name="run" depends="checkversion">
		<echo>Compare "./db/query.fa" (query) against "./db/tursiops.fa" (subject) using "plastp".</echo>
		<echo/>
		<echo>Running PLAST...</echo>
		<java classname="org.inria.genscale.plast.BasicPlastRunner" 
		      fork="yes"
		      output="${basedir}/output.txt"
		      errorproperty="jerror">
         <classpath>
           <pathelement location="${jar.dir}/plast.jar"/>
           <pathelement path="${classes.dir}"/>
         </classpath>
         <jvmarg value="-Djava.library.path=${basedir}/native"/>
       </java>
       <echo>  done.</echo>
       <echo>Results available in: ${basedir}/output.txt</echo>
       <echo unless:true="jerror">${jerror}</echo>
	</target>
	
	<!-- prepare a zip for distribution -->
	<target name="package">
		<delete dir="${pack.dir}"/>
		<mkdir dir="${pack.dir}"/>
		<copy todir="${pack.dir}/src"><!-- source code-->
			<fileset dir="src"/>
		</copy>
		<copy todir="${pack.dir}/thirdparty"><!-- plast jar and dependencies if any-->
			<fileset dir="thirdparty"/>
		</copy>
		<copy todir="${pack.dir}/native"><!-- plast native c++ compiled library -->
			<fileset dir="native"/>
		</copy>
		<copy todir="${pack.dir}/db"><!-- sample fasta files-->
			<fileset dir="db"/>
		</copy>
		<copy file="README" todir="${pack.dir}"/><!-- readme file -->
		<copy file="LICENSE" todir="${pack.dir}"/><!-- license file -->
		<copy file="build.xml" todir="${pack.dir}"/><!-- Ant file -->
		<copy file=".classpath" todir="${pack.dir}"/><!-- Eclipse file -->
		<copy file=".project" todir="${pack.dir}"/><!-- Eclipse file -->
		<zip destfile="${basedir}/plast-java.zip"  basedir="${pack.dir}/.."/>
		<tar destfile="${basedir}/plast-java.tar" basedir="${pack.dir}/.."/>
		<gzip destfile="${basedir}/plast-java.tar.gz" src="${basedir}/plast-java.tar"/>
	</target>
	
	<!-- display some help -->
    <target name="help">
		<echo>Ant targets available are:</echo>
		<echo>  cmp  : compile application</echo>
		<echo>  run  : run application</echo>
		<echo>         (require that 'cmp' target be executed first).</echo>
		<echo/>
		<echo>Requirements: Oracle Java Runtime 1.7 or above.</echo>
		<echo>  PLAST software is not guarantee to work appropriately with</echo>
		<echo>  Java releases *not* provided by Oracle; i.e. avoid using gcj,</echo>
		<echo>  OpenJDK, etc.</echo>
    </target>
</project>