[med-svn] [Git][med-team/logol][master] 5 commits: Depending on biojava-live 1:1.9.5+dfsg, which introduced new jar names
Pierre Gruet (@pgt)
gitlab at salsa.debian.org
Mon Apr 11 07:59:41 BST 2022
Pierre Gruet pushed to branch master at Debian Med / logol
Commits:
74017b0b by Pierre Gruet at 2022-04-10T22:34:03+02:00
Depending on biojava-live 1:1.9.5+dfsg, which introduced new jar names
- - - - -
999ea984 by Pierre Gruet at 2022-04-10T22:35:09+02:00
Rules-Requires-Root: no
- - - - -
edac9eb0 by Pierre Gruet at 2022-04-10T22:35:28+02:00
Raising Standards version to 4.6.0
- - - - -
725a23dd by Pierre Gruet at 2022-04-10T22:49:07+02:00
Updating changelog
- - - - -
ae05911a by Pierre Gruet at 2022-04-11T08:59:14+02:00
Upload to experimental
- - - - -
6 changed files:
- debian/changelog
- debian/control
- debian/patches/fixLibPath
- + debian/patches/fix_biojava_paths_in_scripts.patch
- debian/patches/series
- debian/patches/setDebianDirs
Changes:
=====================================
debian/changelog
=====================================
@@ -1,3 +1,12 @@
+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 at 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
=====================================
debian/control
=====================================
@@ -10,7 +10,7 @@ Build-Depends: debhelper-compat (= 12),
gawk,
swi-prolog (>=8.4.2),
swi-prolog-abi-binary-68,
- libbiojava-java,
+ libbiojava-java (>= 1:1.9.5+dfsg),
antlr3,
libcommons-cli-java,
libcommons-collections3-java,
@@ -29,10 +29,11 @@ Build-Depends: debhelper-compat (= 12),
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
@@ -41,7 +42,7 @@ Depends: ${shlibs:Depends},
default-jre | java7-runtime,
ruby,
gawk,
- libbiojava-java,
+ libbiojava-java (>= 1:1.9.5+dfsg),
antlr3,
libcommons-cli-java,
libcommons-collections3-java,
=====================================
debian/patches/fixLibPath
=====================================
@@ -39,12 +39,13 @@ Last-Updated: 2012-06-18
<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 @@ Last-Updated: 2012-06-18
</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>
=====================================
debian/patches/fix_biojava_paths_in_scripts.patch
=====================================
@@ -0,0 +1,61 @@
+Description: biojava has been split into several jars, starting from version 1.9
+Author: Pierre Gruet <pgt at 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 $*
+
+
=====================================
debian/patches/series
=====================================
@@ -7,3 +7,4 @@ fix_antlr35
fix_swipl_declarations
fix_swipl_foreign_load
remove_test
+fix_biojava_paths_in_scripts.patch
=====================================
debian/patches/setDebianDirs
=====================================
@@ -30,7 +30,7 @@ Last-Updated: 2012-06-18
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 $*
--- a/LogolMultiExec.sh
+++ b/LogolMultiExec.sh
@@ -39,5 +39,5 @@ Last-Updated: 2012-06-18
echo "calling logol with parameters "$*
-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 $*
View it on GitLab: https://salsa.debian.org/med-team/logol/-/compare/79e69286407b68283f7786169bcd0b5c308cdeb0...ae05911a0e454c67d9b7bacfe825e44a3d92f6bc
--
View it on GitLab: https://salsa.debian.org/med-team/logol/-/compare/79e69286407b68283f7786169bcd0b5c308cdeb0...ae05911a0e454c67d9b7bacfe825e44a3d92f6bc
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