Subject: Use debian library for generation
Description: Debian libraries should be used
Author: Olivier Sallou <osallou@debian.org>
Last-Updated: 2012-06-18
--- a/build.xml
+++ b/build.xml
@@ -1,5 +1,5 @@
 <?xml version="1.0" encoding="ISO-8859-1"?>
-<project name="LogolMatch" basedir="." default="create-jar">
+<project name="LogolMatch" basedir="." default="test_swi">
 
 	<property environment="env" />
 
@@ -64,13 +64,16 @@
 		<fileset dir="${basedir}/lib">
 			<patternset refid="java.libs" />
 		</fileset>
+               <fileset dir="/usr/share/java" >
+                       <patternset refid="java.libs" />
+               </fileset>
 	</path>
 
 
 
 	<target name="clean" description="Delete all generated files">
-		<delete dir="${bin.dir}" />
-		<delete>
+		<delete dir="${bin.dir}" quiet="true" />
+		<delete quiet="true">
 			<fileset dir="${test.dir}/tmp">
 				<include name="*"/>
 			</fileset>
@@ -139,6 +142,8 @@
 
 	<target name="test_swi" description="unit test with swi-prolog"
 		depends="setup,compile_swi_exe,create-jar">
+		<mkdir dir="test/tmp" />
+		<mkdir dir="test/results" />
 		<exec executable="swipl">
 			<arg line=" -f ${basedir}/prolog/unitTest/swi-unit.pl -- ${basedir}/prolog/unitTest/sampleUnit.pro ${basedir}/prolog/sicstus.pl ${work.dir}/SwiLogolSelfTest-PUnit-${build.nb}.xml ${basedir}/prolog/unitTest/plunittest.pro ${basedir}/prolog/logol.pl ${basedir}/test/test.fasta" />
 		</exec>
@@ -148,6 +153,26 @@
 				<fileset dir="${basedir}/lib">
 					<include name="**/*.jar" />
 				</fileset>
+                               <fileset dir="/usr/share/java" >
+                                       <include name="biojava-bytecode.jar"/>
+                                       <include name="biojava-core.jar"/>
+                                       <include name="activation.jar"/>
+                                       <include name="bytecode.jar"/>
+                                       <include name="drmaa.jar"/>
+                                       <include name="antlr3-runtime.jar"/>
+                                       <include name="commons-cli.jar"/>
+                                       <include name="commons-lang.jar"/>
+                                       <include name="commons-collections3.jar"/>
+                                       <include name="commons-configuration.jar"/>
+                                       <include name="commons-logging.jar"/>
+                                       <include name="xalan2.jar"/>
+                                       <include name="xercesImpl.jar"/>
+                                       <include name="xml-apis.jar"/>
+                                       <include name="javax.mail.jar"/>
+                                       <include name="log4j-1.2.jar"/>
+                                       <include name="serializer.jar"/>
+                                       <include name="junit4.jar"/>
+                               </fileset>
 			</classpath>
 			<sysproperty key="logol.install" value="${basedir}" />
 			<sysproperty key="log4j.configuration" value="file://${basedir}/log4j.properties" />
@@ -210,6 +235,7 @@
 				<attribute name="Main-Class" value="org.irisa.genouest.logol.Logol" />
 				<attribute name="Implementation-Version" value="${version}" />
 				<attribute name="Implementation-Build" value="${build.nb}" />
+                                <attribute name="Class-Path" value="/usr/share/java/biojava-bytecode.jar /usr/share/java/biojava-core.jar /usr/share/java/activation.jar /usr/share/java/bytecode.jar /usr/share/java/serializer.jar /usr/share/java/antlr3-runtime.jar /usr/share/java/drmaa.jar /usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar /usr/share/java/commons-configuration.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-logging.jar /usr/share/java/xalan2.jar /usr/share/java/xercesImpl.jar /usr/share/java/javax.mail.jar /usr/share/java/log4j1.2.jar /usr/share/java/xml-apis.jar" />
 			</manifest>
 		</jar>
 	</target>
--- a/log4j.properties
+++ b/log4j.properties
@@ -13,6 +13,6 @@
 
 
 log4j.appender.A2=org.apache.log4j.FileAppender
-log4j.appender.A2.File=/tmp/logol.log
+log4j.appender.A2.File=/var/log/logol/logol.log
 log4j.appender.A2.layout=org.apache.log4j.PatternLayout
 log4j.appender.A2.layout.ConversionPattern=%d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - %m%n
