diff -Nru logol-1.7.9+dfsg/debian/changelog logol-1.7.9+dfsg/debian/changelog
--- logol-1.7.9+dfsg/debian/changelog	2022-03-07 22:14:23.000000000 +0000
+++ logol-1.7.9+dfsg/debian/changelog	2022-04-11 14:38:53.000000000 +0000
@@ -1,8 +1,32 @@
-logol (1.7.9+dfsg-1build1) jammy; urgency=medium
+logol (1.7.9+dfsg-5) unstable; urgency=medium
 
-  * No-change rebuild after swi-prolog ABI change. 
+  * Team upload
+  * Upload to unstable to accompany auto-biojava-live transition
+    (Closes: #1009295)
 
- -- Michael Hudson-Doyle <michael.hudson@ubuntu.com>  Tue, 08 Mar 2022 11:14:23 +1300
+ -- Pierre Gruet <pgt@debian.org>  Mon, 11 Apr 2022 16:38:53 +0200
+
+logol (1.7.9+dfsg-4) experimental; urgency=medium
+
+  * Team upload
+  * Depending on biojava-live 1:1.9.5+dfsg, which introduced new jar names
+  * Raising Standards version to 4.6.0:
+    - Rules-Requires-Root: no
+
+ -- Pierre Gruet <pgt@debian.org>  Sun, 10 Apr 2022 22:50:07 +0200
+
+logol (1.7.9+dfsg-3) unstable; urgency=medium
+
+  * d/control: add dep on swi-prolog ABI via  swi-prolog-abi-binary-68 
+
+ -- Olivier Sallou <osallou@debian.org>  Fri, 04 Mar 2022 06:29:09 +0000
+
+logol (1.7.9+dfsg-2) unstable; urgency=medium
+
+  * Source only upload, rebuilding against swi-prolog/8.4.2+dfsg-2 after
+    swi-prolog ABI break (Closes: #1006384).
+
+ -- Olivier Sallou <osallou@debian.org>  Tue, 01 Mar 2022 08:54:23 +0000
 
 logol (1.7.9+dfsg-1) unstable; urgency=medium
 
diff -Nru logol-1.7.9+dfsg/debian/control logol-1.7.9+dfsg/debian/control
--- logol-1.7.9+dfsg/debian/control	2021-08-16 10:28:14.000000000 +0000
+++ logol-1.7.9+dfsg/debian/control	2022-04-10 20:35:18.000000000 +0000
@@ -8,8 +8,9 @@
                ant,
                ruby,
                gawk,
-               swi-prolog,
-               libbiojava-java,
+               swi-prolog (>=8.4.2),
+               swi-prolog-abi-binary-68,
+               libbiojava-java (>= 1:1.9.5+dfsg),
                antlr3,
                libcommons-cli-java,
                libcommons-collections3-java,
@@ -28,10 +29,11 @@
                cassiopee,
                ruby-cassiopee,
                chrpath
-Standards-Version: 4.5.0
+Standards-Version: 4.6.0
 Vcs-Browser: https://salsa.debian.org/med-team/logol
 Vcs-Git: https://salsa.debian.org/med-team/logol.git
 Homepage: http://logol.genouest.org
+Rules-Requires-Root: no
 
 Package: logol
 Architecture: all
@@ -40,7 +42,7 @@
          default-jre | java7-runtime,
          ruby,
          gawk,
-         libbiojava-java,
+         libbiojava-java (>= 1:1.9.5+dfsg),
          antlr3,
          libcommons-cli-java,
          libcommons-collections3-java,
@@ -64,7 +66,8 @@
 Architecture: any
 Depends: ${shlibs:Depends},
          ${misc:Depends},
-         swi-prolog
+         swi-prolog,
+         swi-prolog-abi-binary-68
 Description: Pattern matching tool using Logol language
  This package contains the Prolog binaries used by Logol to parse
  the sequence and match the grammar.
diff -Nru logol-1.7.9+dfsg/debian/patches/fix_biojava_paths_in_scripts.patch logol-1.7.9+dfsg/debian/patches/fix_biojava_paths_in_scripts.patch
--- logol-1.7.9+dfsg/debian/patches/fix_biojava_paths_in_scripts.patch	1970-01-01 00:00:00.000000000 +0000
+++ logol-1.7.9+dfsg/debian/patches/fix_biojava_paths_in_scripts.patch	2022-04-10 20:32:04.000000000 +0000
@@ -0,0 +1,61 @@
+Description: biojava has been split into several jars, starting from version 1.9
+Author: Pierre Gruet <pgt@debian.org>
+Forwarded: not-needed
+Last-Update: 2022-02-28
+
+--- a/LogolExec.rb
++++ b/LogolExec.rb
+@@ -10,7 +10,7 @@
+ 
+ #puts "calling logol with parameters "+args
+ 
+-cmd="java -Xms512m -Xmx1024m  -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath  $LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.3.jar  org.irisa.genouest.logol.Logol "+args.to_s
++cmd="java -Xms512m -Xmx1024m  -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath  /usr/share/java/biojava-bytecode.jar:/usr/share/java/biojava-core.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.3.jar  org.irisa.genouest.logol.Logol "+args.to_s
+ cmd=cmd.gsub(":",";")
+ cmd=cmd.gsub("file;","file:")
+ cmd=cmd.gsub("$LOGOL_HOME",LOGOL_HOME)
+--- a/LogolMultiExec.rb
++++ b/LogolMultiExec.rb
+@@ -10,7 +10,7 @@
+ 
+ #puts "calling logol with parameters "+args
+ 
+-cmd="java -Xms512m -Xmx1024m  -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath  $LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.3.jar  org.irisa.genouest.logol.dispatcher.Dispatch "+args.to_s
++cmd="java -Xms512m -Xmx1024m  -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath  /usr/share/java/biojava-bytecode.jar:/usr/share/java/biojava-core.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.3.jar  org.irisa.genouest.logol.dispatcher.Dispatch "+args.to_s
+ cmd=cmd.gsub(":",";")
+ cmd=cmd.gsub("file;","file:")
+ cmd=cmd.gsub("$LOGOL_HOME",LOGOL_HOME)
+--- a/MatchToModel.sh
++++ b/MatchToModel.sh
+@@ -16,7 +16,7 @@
+ echo "calling logol with parameters "$*
+ 
+ java -Xms512m -Xmx4096m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -
+-classpath  $LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/li
+-b/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_
+-HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL
+-_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar  org.irisa.genouest.logol.utils.model.MatchToModel $*
+\ No newline at end of file
++classpath  /usr/share/java/biojava-bytecode.jar:/usr/share/java/biojava-core.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.ja
++r:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5
++.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL
++_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar  org.irisa.genouest.logol.utils.model.MatchToModel $*
+--- a/Model2Grammar.sh
++++ b/Model2Grammar.sh
+@@ -14,5 +14,5 @@
+ 
+ echo "calling logol with parameters "$*
+ 
+-java -Xms512m -Xmx4096m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath  $LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar  org.irisa.genouest.logol.utils.model.ModelConverter $*
++java -Xms512m -Xmx4096m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath  /usr/share/java/biojava-bytecode.jar:/usr/share/java/biojava-core.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar  org.irisa.genouest.logol.utils.model.ModelConverter $*
+ 
+--- a/logolTest.sh
++++ b/logolTest.sh
+@@ -11,6 +11,6 @@
+ 
+ echo "calling logol with parameters "$*
+ 
+-java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath   $LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/junit.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar  org.irisa.genouest.logol.test.TestSuite  $*
++java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath   /usr/share/java/biojava-bytecode.jar:/usr/share/java/biojava-core.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/junit.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.jar  org.irisa.genouest.logol.test.TestSuite  $*
+ 
+ 
diff -Nru logol-1.7.9+dfsg/debian/patches/fixLibPath logol-1.7.9+dfsg/debian/patches/fixLibPath
--- logol-1.7.9+dfsg/debian/patches/fixLibPath	2021-08-16 10:28:14.000000000 +0000
+++ logol-1.7.9+dfsg/debian/patches/fixLibPath	2022-04-10 20:32:04.000000000 +0000
@@ -39,12 +39,13 @@
  		<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 ${basedir}/test/test.fasta" />
  		</exec>
-@@ -148,6 +153,25 @@
+@@ -148,6 +153,26 @@
  				<fileset dir="${basedir}/lib">
  					<include name="**/*.jar" />
  				</fileset>
 +                               <fileset dir="/usr/share/java" >
-+                                       <include name="biojava.jar"/>
++                                       <include name="biojava-bytecode.jar"/>
++                                       <include name="biojava-core.jar"/>
 +                                       <include name="activation.jar"/>
 +                                       <include name="bytecode.jar"/>
 +                                       <include name="drmaa.jar"/>
@@ -65,11 +66,11 @@
  			</classpath>
  			<sysproperty key="logol.install" value="${basedir}" />
  			<sysproperty key="log4j.configuration" value="file://${basedir}/log4j.properties" />
-@@ -210,6 +234,7 @@
+@@ -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.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" />
++                                <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>
diff -Nru logol-1.7.9+dfsg/debian/patches/series logol-1.7.9+dfsg/debian/patches/series
--- logol-1.7.9+dfsg/debian/patches/series	2021-08-16 10:28:14.000000000 +0000
+++ logol-1.7.9+dfsg/debian/patches/series	2022-04-10 20:32:04.000000000 +0000
@@ -7,3 +7,4 @@
 fix_swipl_declarations
 fix_swipl_foreign_load
 remove_test
+fix_biojava_paths_in_scripts.patch
diff -Nru logol-1.7.9+dfsg/debian/patches/setDebianDirs logol-1.7.9+dfsg/debian/patches/setDebianDirs
--- logol-1.7.9+dfsg/debian/patches/setDebianDirs	2021-08-16 10:28:14.000000000 +0000
+++ logol-1.7.9+dfsg/debian/patches/setDebianDirs	2022-04-10 20:32:04.000000000 +0000
@@ -30,7 +30,7 @@
  fi
  
 -java $JAVA_OPTS  -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath  $LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.3.jar  org.irisa.genouest.logol.Logol  $*
-+java -Xms512m -Xmx1024m  -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath  $LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli.jar:$LOGOL_HOME/lib/commons-collections.jar:$LOGOL_HOME/lib/commons-lang.jar:$LOGOL_HOME/lib/commons-logging.jar:$LOGOL_HOME/lib/log4j-1.2.jar:$LOGOL_HOME/lib/antlr.jar  org.irisa.genouest.logol.Logol  $*
++java -Xms512m -Xmx1024m  -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath  /usr/share/java/biojava-bytecode.jar:/usr/share/java/biojava-core.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/serializer.jar:$LOGOL_HOME/lib/commons-configuration.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli.jar:$LOGOL_HOME/lib/commons-collections.jar:$LOGOL_HOME/lib/commons-lang.jar:$LOGOL_HOME/lib/commons-logging.jar:$LOGOL_HOME/lib/log4j-1.2.jar:$LOGOL_HOME/lib/antlr.jar  org.irisa.genouest.logol.Logol  $*
  
 --- a/LogolMultiExec.sh
 +++ b/LogolMultiExec.sh
@@ -39,5 +39,5 @@
  echo "calling logol with parameters "$*
  
 -java $JAVA_OPTS -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath  $LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/drmaa.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.3.jar  org.irisa.genouest.logol.dispatcher.Dispatch  $*
-+java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath  $LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/drmaa.jar:$LOGOL_HOME/lib/commons-configuration.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli.jar:$LOGOL_HOME/lib/commons-collections.jar:$LOGOL_HOME/lib/commons-lang.jar:$LOGOL_HOME/lib/commons-logging.jar:$LOGOL_HOME/lib/log4j-1.2.jar:$LOGOL_HOME/lib/antlr.jar  org.irisa.genouest.logol.dispatcher.Dispatch  $*
++java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath  $LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:/usr/share/java/biojava-bytecode.jar:/usr/share/java/biojava-core.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/drmaa.jar:$LOGOL_HOME/lib/commons-configuration.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli.jar:$LOGOL_HOME/lib/commons-collections.jar:$LOGOL_HOME/lib/commons-lang.jar:$LOGOL_HOME/lib/commons-logging.jar:$LOGOL_HOME/lib/log4j-1.2.jar:$LOGOL_HOME/lib/antlr.jar  org.irisa.genouest.logol.dispatcher.Dispatch  $*