Author: osallou Date: 2014-04-18 13:19:24 +0000 (Fri, 18 Apr 2014) New Revision: 16728
Added: trunk/packages/logol/tags/1.7.0-1/ trunk/packages/logol/tags/1.7.0-1/debian/changelog trunk/packages/logol/tags/1.7.0-1/debian/control trunk/packages/logol/tags/1.7.0-1/debian/patches/fixLibPath trunk/packages/logol/tags/1.7.0-1/debian/patches/setDebianDirs Removed: trunk/packages/logol/tags/1.7.0-1/debian/changelog trunk/packages/logol/tags/1.7.0-1/debian/control trunk/packages/logol/tags/1.7.0-1/debian/patches/fixLibPath trunk/packages/logol/tags/1.7.0-1/debian/patches/setDebianDirs Log: [svn-buildpackage] Tagging logol 1.7.0-1 Deleted: trunk/packages/logol/tags/1.7.0-1/debian/changelog =================================================================== --- trunk/packages/logol/trunk/debian/changelog 2014-04-17 15:03:09 UTC (rev 16722) +++ trunk/packages/logol/tags/1.7.0-1/debian/changelog 2014-04-18 13:19:24 UTC (rev 16728) @@ -1,126 +0,0 @@ -logol (1.6.10-1) unstable; urgency=low - - * New upstream release, fix bug on Hamming error search - - -- Olivier Sallou <[email protected]> Sat, 08 Feb 2014 13:17:17 +0100 - -logol (1.6.9-3) unstable; urgency=low - - * d/control,d/patches: Remove rubygems dependency, thanks to - Cédric Boutillier <[email protected]> (Closes: #735579). - * Upgrade to Standards 3.9.5. - - -- Olivier Sallou <[email protected]> Fri, 17 Jan 2014 09:07:38 +0100 - -logol (1.6.9-2) unstable; urgency=low - - * Fix prolog doc generation (Closes: #730916). - - -- Olivier Sallou <[email protected]> Sun, 01 Dec 2013 11:55:42 +0100 - -logol (1.6.9-1) unstable; urgency=low - - * New upstream release (bug fixes, add Windows support - for Sicstus 4.2.x and Swi-prolog). - - -- Olivier Sallou <[email protected]> Mon, 11 Nov 2013 10:11:17 +0100 - -logol (1.6.6-1) unstable; urgency=low - - * New upstream releas (bug fixes on morphisms and doc). - - -- Olivier Sallou <[email protected]> Wed, 30 Oct 2013 16:21:09 +0100 - -logol (1.6.5-1) unstable; urgency=low - - * New upstream release (memory footprint optimisation in some cases). - - -- Olivier Sallou <[email protected]> Fri, 25 Oct 2013 13:48:22 +0200 - -logol (1.6.4-1) unstable; urgency=low - - * New upstream release fixing bugs - - -- Olivier Sallou <[email protected]> Tue, 22 Oct 2013 08:35:45 +0200 - -logol (1.6.3-1) unstable; urgency=low - - * New upstream release fixing important bugs on distance search - * Remove patch for doc generation after swi-prolog fix - - -- Olivier Sallou <[email protected]> Mon, 02 Sep 2013 08:54:46 +0200 - -logol (1.6.2-3) unstable; urgency=low - - * Fix swi-prolog compilation (Closes: #719030). - - -- Olivier Sallou <[email protected]> Thu, 08 Aug 2013 10:30:12 +0200 - -logol (1.6.2-2) unstable; urgency=low - - [ Olivier Sallou ] - * Remove deprecated DM-Upload field. - - [ Dmitrijs Ledkovs ] - * Bump standards version to 3.9.4. - * Remove empty postinst script. - * Add dependancy on texlive-latex-extra, needed to fix documentation - FTBFS with new TeX Live. - - -- Dmitrijs Ledkovs <[email protected]> Mon, 03 Jun 2013 23:36:49 +0100 - -logol (1.6.2-1) unstable; urgency=low - - * New upstream release (bug fixes) - - -- Olivier Sallou <[email protected]> Fri, 24 May 2013 14:37:24 +0200 - -logol (1.6.1-1) unstable; urgency=low - - * New upstream release (bug fixes) - - -- Olivier Sallou <[email protected]> Tue, 09 Apr 2013 16:57:33 +0200 - -logol (1.6.0-1) unstable; urgency=low - - * New upstream release with bug fixes - - -- Olivier Sallou <[email protected]> Fri, 15 Feb 2013 10:05:50 +0100 - -logol (1.5.0-6) unstable; urgency=low - - [ Olivier Sallou ] - * debian/control: Fix typo in description (Closes: #685079). - Thanks to Erik Esterer <[email protected]> - - -- Olivier Sallou <[email protected]> Fri, 17 Aug 2012 08:00:58 +0200 - -logol (1.5.0-5) unstable; urgency=low - - [ Olivier Sallou] - * Transition package to use default java implementation: - From [email protected] (Closes: #684158) - - d/control: BD on default-jdk (>= 1:1.6), switch runtime dependency - to default-jre | java6-runtime. - - d/rules: Specify source/target = 1.5 to ensure backwards compatible - bytecode is built. - - -- Olivier Sallou <[email protected]> Tue, 07 Aug 2012 15:18:43 +0200 - -logol (1.5.0-4) unstable; urgency=low - - * debian/postinst: remove directory permissions (Closes: #683647). - - -- Olivier Sallou <[email protected]> Thu, 02 Aug 2012 17:09:31 +0200 - -logol (1.5.0-2) unstable; urgency=low - - * Support Arch dependent and arch independent separate builds. - - -- Olivier Sallou <[email protected]> Sun, 01 Jul 2012 23:49:16 +0200 - -logol (1.5.0-1) unstable; urgency=low - - * Initial release (Closes: #678373). - - -- Olivier Sallou <[email protected]> Thu, 21 Jun 2012 12:50:22 +0200 Copied: trunk/packages/logol/tags/1.7.0-1/debian/changelog (from rev 16727, trunk/packages/logol/trunk/debian/changelog) =================================================================== --- trunk/packages/logol/tags/1.7.0-1/debian/changelog (rev 0) +++ trunk/packages/logol/tags/1.7.0-1/debian/changelog 2014-04-18 13:19:24 UTC (rev 16728) @@ -0,0 +1,132 @@ +logol (1.7.0-1) unstable; urgency=low + + * New upstream release + + -- Olivier Sallou <[email protected]> Sat, 08 Feb 2014 13:25:38 +0100 + +logol (1.6.10-1) unstable; urgency=low + + * New upstream release, fix bug on Hamming error search + + -- Olivier Sallou <[email protected]> Sat, 08 Feb 2014 13:17:17 +0100 + +logol (1.6.9-3) unstable; urgency=low + + * d/control,d/patches: Remove rubygems dependency, thanks to + Cédric Boutillier <[email protected]> (Closes: #735579). + * Upgrade to Standards 3.9.5. + + -- Olivier Sallou <[email protected]> Fri, 17 Jan 2014 09:07:38 +0100 + +logol (1.6.9-2) unstable; urgency=low + + * Fix prolog doc generation (Closes: #730916). + + -- Olivier Sallou <[email protected]> Sun, 01 Dec 2013 11:55:42 +0100 + +logol (1.6.9-1) unstable; urgency=low + + * New upstream release (bug fixes, add Windows support + for Sicstus 4.2.x and Swi-prolog). + + -- Olivier Sallou <[email protected]> Mon, 11 Nov 2013 10:11:17 +0100 + +logol (1.6.6-1) unstable; urgency=low + + * New upstream releas (bug fixes on morphisms and doc). + + -- Olivier Sallou <[email protected]> Wed, 30 Oct 2013 16:21:09 +0100 + +logol (1.6.5-1) unstable; urgency=low + + * New upstream release (memory footprint optimisation in some cases). + + -- Olivier Sallou <[email protected]> Fri, 25 Oct 2013 13:48:22 +0200 + +logol (1.6.4-1) unstable; urgency=low + + * New upstream release fixing bugs + + -- Olivier Sallou <[email protected]> Tue, 22 Oct 2013 08:35:45 +0200 + +logol (1.6.3-1) unstable; urgency=low + + * New upstream release fixing important bugs on distance search + * Remove patch for doc generation after swi-prolog fix + + -- Olivier Sallou <[email protected]> Mon, 02 Sep 2013 08:54:46 +0200 + +logol (1.6.2-3) unstable; urgency=low + + * Fix swi-prolog compilation (Closes: #719030). + + -- Olivier Sallou <[email protected]> Thu, 08 Aug 2013 10:30:12 +0200 + +logol (1.6.2-2) unstable; urgency=low + + [ Olivier Sallou ] + * Remove deprecated DM-Upload field. + + [ Dmitrijs Ledkovs ] + * Bump standards version to 3.9.4. + * Remove empty postinst script. + * Add dependancy on texlive-latex-extra, needed to fix documentation + FTBFS with new TeX Live. + + -- Dmitrijs Ledkovs <[email protected]> Mon, 03 Jun 2013 23:36:49 +0100 + +logol (1.6.2-1) unstable; urgency=low + + * New upstream release (bug fixes) + + -- Olivier Sallou <[email protected]> Fri, 24 May 2013 14:37:24 +0200 + +logol (1.6.1-1) unstable; urgency=low + + * New upstream release (bug fixes) + + -- Olivier Sallou <[email protected]> Tue, 09 Apr 2013 16:57:33 +0200 + +logol (1.6.0-1) unstable; urgency=low + + * New upstream release with bug fixes + + -- Olivier Sallou <[email protected]> Fri, 15 Feb 2013 10:05:50 +0100 + +logol (1.5.0-6) unstable; urgency=low + + [ Olivier Sallou ] + * debian/control: Fix typo in description (Closes: #685079). + Thanks to Erik Esterer <[email protected]> + + -- Olivier Sallou <[email protected]> Fri, 17 Aug 2012 08:00:58 +0200 + +logol (1.5.0-5) unstable; urgency=low + + [ Olivier Sallou] + * Transition package to use default java implementation: + From [email protected] (Closes: #684158) + - d/control: BD on default-jdk (>= 1:1.6), switch runtime dependency + to default-jre | java6-runtime. + - d/rules: Specify source/target = 1.5 to ensure backwards compatible + bytecode is built. + + -- Olivier Sallou <[email protected]> Tue, 07 Aug 2012 15:18:43 +0200 + +logol (1.5.0-4) unstable; urgency=low + + * debian/postinst: remove directory permissions (Closes: #683647). + + -- Olivier Sallou <[email protected]> Thu, 02 Aug 2012 17:09:31 +0200 + +logol (1.5.0-2) unstable; urgency=low + + * Support Arch dependent and arch independent separate builds. + + -- Olivier Sallou <[email protected]> Sun, 01 Jul 2012 23:49:16 +0200 + +logol (1.5.0-1) unstable; urgency=low + + * Initial release (Closes: #678373). + + -- Olivier Sallou <[email protected]> Thu, 21 Jun 2012 12:50:22 +0200 Deleted: trunk/packages/logol/tags/1.7.0-1/debian/control =================================================================== --- trunk/packages/logol/trunk/debian/control 2014-04-17 15:03:09 UTC (rev 16722) +++ trunk/packages/logol/tags/1.7.0-1/debian/control 2014-04-18 13:19:24 UTC (rev 16728) @@ -1,44 +0,0 @@ -Source: logol -Section: science -Priority: optional -Maintainer: Debian Med Packaging Team <[email protected]> -Uploaders: Olivier Sallou <[email protected]> -Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/logol/trunk/ -Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/logol/ -Build-Depends: debhelper (>= 8.0.0),default-jdk (>= 1:1.6),ant,ruby, - gawk, swi-prolog (>=6.4.1-3), - libbiojava-java, libdrmaa-java, antlr3, libcommons-cli-java, - libcommons-collections3-java, libcommons-configuration-java, - libcommons-lang-java, libcommons-logging-java, libxalan2-java, - libxerces2-java, junit4, libgnumail-java, - liblog4j1.2-java,texlive, texlive-latex-extra, tex4ht, - libncursesw5-dev, ruby-cassiopee (>=0.1.12), ant-optional -Standards-Version: 3.9.5 -Homepage: http://logol.genouest.org - -Package: logol -Architecture: all -Depends: ${shlibs:Depends}, ${misc:Depends}, default-jre | java6-runtime, - ruby, gawk, - libbiojava-java, libdrmaa-java, antlr3, libcommons-cli-java, - libcommons-collections3-java, libcommons-configuration-java, - libcommons-lang-java, libcommons-logging-java, libxalan2-java, - libxerces2-java, libgnumail-java, liblog4j1.2-java, - ruby-cassiopee (>=0.1.12), logol-bin -Description: Pattern matching tool using Logol language - Logol is a pattern matching tool using the Logol language. - It searches with a specific grammar a pattern in small - or large sequence (dna, rna, protein). It provides complete - result matching with the original grammar in the results. - -Package: logol-bin -Architecture: any -Depends: ${shlibs:Depends}, ${misc:Depends}, swi-prolog(>=6.4.1-3), libncursesw5 -Description: Pattern matching tool using Logol language - This package contains the Prolog binaries used by Logol to parse - the sequence and match the grammar. - . - Logol is a pattern matching tool using the Logol language. - It searches with a specific grammar a pattern in small - or large sequence (dna, rna, protein). It provides complete - result matching with the original grammar in the results. Copied: trunk/packages/logol/tags/1.7.0-1/debian/control (from rev 16726, trunk/packages/logol/trunk/debian/control) =================================================================== --- trunk/packages/logol/tags/1.7.0-1/debian/control (rev 0) +++ trunk/packages/logol/tags/1.7.0-1/debian/control 2014-04-18 13:19:24 UTC (rev 16728) @@ -0,0 +1,46 @@ +Source: logol +Section: science +Priority: optional +Maintainer: Debian Med Packaging Team <[email protected]> +Uploaders: Olivier Sallou <[email protected]> +Vcs-Svn: svn://anonscm.debian.org/debian-med/trunk/packages/logol/trunk/ +Vcs-Browser: http://anonscm.debian.org/viewvc/debian-med/trunk/packages/logol/ +Build-Depends: debhelper (>= 8.0.0),default-jdk (>= 1:1.6),ant,ruby, + gawk, swi-prolog (>=6.4.1-3), + libbiojava-java, libdrmaa-java, antlr3, libcommons-cli-java, + libcommons-collections3-java, libcommons-configuration-java, + libcommons-lang-java, libcommons-logging-java, libxalan2-java, + libxerces2-java, junit4, libgnumail-java, + liblog4j1.2-java,texlive, texlive-latex-extra, tex4ht, + libncursesw5-dev, ant-optional, + cassiopee, ruby-cassiopee +Standards-Version: 3.9.5 +Homepage: http://logol.genouest.org + +Package: logol +Architecture: all +Depends: ${shlibs:Depends}, ${misc:Depends}, default-jre | java7-runtime, + ruby, gawk, + libbiojava-java, libdrmaa-java, antlr3, libcommons-cli-java, + libcommons-collections3-java, libcommons-configuration-java, + libcommons-lang-java, libcommons-logging-java, libxalan2-java, + libxerces2-java, libgnumail-java, liblog4j1.2-java, + cassiopee, logol-bin +Suggests: ruby-cassiopee (>=0.1.12) +Description: Pattern matching tool using Logol language + Logol is a pattern matching tool using the Logol language. + It searches with a specific grammar a pattern in small + or large sequence (dna, rna, protein). It provides complete + result matching with the original grammar in the results. + +Package: logol-bin +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends}, swi-prolog(>=6.4.1-3), libncursesw5 +Description: Pattern matching tool using Logol language + This package contains the Prolog binaries used by Logol to parse + the sequence and match the grammar. + . + Logol is a pattern matching tool using the Logol language. + It searches with a specific grammar a pattern in small + or large sequence (dna, rna, protein). It provides complete + result matching with the original grammar in the results. Deleted: trunk/packages/logol/tags/1.7.0-1/debian/patches/fixLibPath =================================================================== --- trunk/packages/logol/trunk/debian/patches/fixLibPath 2014-04-17 15:03:09 UTC (rev 16722) +++ trunk/packages/logol/tags/1.7.0-1/debian/patches/fixLibPath 2014-04-18 13:19:24 UTC (rev 16728) @@ -1,57 +0,0 @@ -Subject: Use debian library for generation -Description: Debian libraries should be used -Author: Olivier Sallou <[email protected]> -Last-Updated: 2012-06-18 ---- a/build.xml -+++ b/build.xml -@@ -1,5 +1,5 @@ - <?xml version="1.0" encoding="ISO-8859-1"?> --<project name="LogolMatch" basedir="." default="create-jar"> -+<project name="LogolMatch" basedir="." default="test_swi"> - - <property environment="env" /> - -@@ -57,6 +57,9 @@ - <fileset dir="${basedir}/lib"> - <patternset refid="java.libs" /> - </fileset> -+ <fileset dir="/usr/share/java" > -+ <patternset refid="java.libs" /> -+ </fileset> - </path> - - -@@ -141,6 +144,25 @@ - <fileset dir="${basedir}/lib"> - <include name="**/*.jar" /> - </fileset> -+ <fileset dir="/usr/share/java" > -+ <include name="biojava.jar"/> -+ <include name="activation.jar"/> -+ <include name="bytecode.jar"/> -+ <include name="drmaa.jar"/> -+ <include name="antlr3-runtime.jar"/> -+ <include name="commons-cli.jar"/> -+ <include name="commons-lang.jar"/> -+ <include name="commons-collections3.jar"/> -+ <include name="commons-configuration.jar"/> -+ <include name="commons-logging.jar"/> -+ <include name="xalan2.jar"/> -+ <include name="xercesImpl.jar"/> -+ <include name="xml-apis.jar"/> -+ <include name="gnumail.jar"/> -+ <include name="log4j-1.2.jar"/> -+ <include name="serializer.jar"/> -+ <include name="junit4.jar"/> -+ </fileset> - </classpath> - <sysproperty key="logol.install" value="${basedir}" /> - <sysproperty key="log4j.configuration" value="file://${basedir}/log4j.properties" /> -@@ -200,6 +222,7 @@ - <attribute name="Main-Class" value="org.irisa.genouest.logol.Logol" /> - <attribute name="Implementation-Version" value="${version}" /> - <attribute name="Implementation-Build" value="${build.nb}" /> -+ <attribute name="Class-Path" value="/usr/share/java/biojava.jar /usr/share/java/activation.jar /usr/share/java/bytecode.jar /usr/share/java/serializer.jar /usr/share/java/antlr3-runtime.jar /usr/share/java/drmaa.jar /usr/share/java/commons-cli.jar /usr/share/java/commons-collections3.jar /usr/share/java/commons-configuration.jar /usr/share/java/commons-lang.jar /usr/share/java/commons-logging.jar /usr/share/java/xalan2.jar /usr/share/java/xercesImpl.jar /usr/share/java/gnumail.jar /usr/share/java/log4j1.2.jar /usr/share/java/xml-apis.jar" /> - </manifest> - </jar> - </target> Copied: trunk/packages/logol/tags/1.7.0-1/debian/patches/fixLibPath (from rev 16725, trunk/packages/logol/trunk/debian/patches/fixLibPath) =================================================================== --- trunk/packages/logol/tags/1.7.0-1/debian/patches/fixLibPath (rev 0) +++ trunk/packages/logol/tags/1.7.0-1/debian/patches/fixLibPath 2014-04-18 13:19:24 UTC (rev 16728) @@ -0,0 +1,57 @@ +Subject: Use debian library for generation +Description: Debian libraries should be used +Author: Olivier Sallou <[email protected]> +Last-Updated: 2012-06-18 +--- a/build.xml ++++ b/build.xml +@@ -1,5 +1,5 @@ + <?xml version="1.0" encoding="ISO-8859-1"?> +-<project name="LogolMatch" basedir="." default="create-jar"> ++<project name="LogolMatch" basedir="." default="test_swi"> + + <property environment="env" /> + +@@ -64,6 +64,9 @@ + <fileset dir="${basedir}/lib"> + <patternset refid="java.libs" /> + </fileset> ++ <fileset dir="/usr/share/java" > ++ <patternset refid="java.libs" /> ++ </fileset> + </path> + + +@@ -148,6 +151,25 @@ + <fileset dir="${basedir}/lib"> + <include name="**/*.jar" /> + </fileset> ++ <fileset dir="/usr/share/java" > ++ <include name="biojava.jar"/> ++ <include name="activation.jar"/> ++ <include name="bytecode.jar"/> ++ <include name="drmaa.jar"/> ++ <include name="antlr3-runtime.jar"/> ++ <include name="commons-cli.jar"/> ++ <include name="commons-lang.jar"/> ++ <include name="commons-collections3.jar"/> ++ <include name="commons-configuration.jar"/> ++ <include name="commons-logging.jar"/> ++ <include name="xalan2.jar"/> ++ <include name="xercesImpl.jar"/> ++ <include name="xml-apis.jar"/> ++ <include name="gnumail.jar"/> ++ <include name="log4j-1.2.jar"/> ++ <include name="serializer.jar"/> ++ <include name="junit4.jar"/> ++ </fileset> + </classpath> + <sysproperty key="logol.install" value="${basedir}" /> + <sysproperty key="log4j.configuration" value="file://${basedir}/log4j.properties" /> +@@ -210,6 +232,7 @@ + <attribute name="Main-Class" value="org.irisa.genouest.logol.Logol" /> + <attribute name="Implementation-Version" value="${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/gnumail.jar /usr/share/java/log4j1.2.jar /usr/share/java/xml-apis.jar" /> + </manifest> + </jar> + </target> Deleted: trunk/packages/logol/tags/1.7.0-1/debian/patches/setDebianDirs =================================================================== --- trunk/packages/logol/trunk/debian/patches/setDebianDirs 2014-04-17 15:03:09 UTC (rev 16722) +++ trunk/packages/logol/tags/1.7.0-1/debian/patches/setDebianDirs 2014-04-18 13:19:24 UTC (rev 16728) @@ -1,55 +0,0 @@ -Subject: Use debian dirs for logs -Description: Debian policy hierarchy use -Author: Olivier Sallou <[email protected]> -Last-Updated: 2012-06-18 ---- a/log4j.properties -+++ b/log4j.properties -@@ -13,6 +13,6 @@ - - - log4j.appender.A2=org.apache.log4j.FileAppender --log4j.appender.A2.File=/home/osallou/CODE/TEST/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 -\ No newline at end of file -+log4j.appender.A2.layout.ConversionPattern=%d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - %m%n ---- a/prolog/logol.properties -+++ b/prolog/logol.properties -@@ -11,9 +11,9 @@ - #maxMatchSize=30000 - maxMatchSize=0 - # Temporary directory used for the analysis. Should be local to the node --workingDir=/tmp/Logol -+workingDir=/tmp/ - # Directory where to place the results. In case of cluster usage, result must be a shared directory between nodes --dir.result=/tmp/Logol -+dir.result=/var/lib/logol/results/ - # Maximum length of a spacer when looking forward for a match - #maxSpacerLength=10000 - maxSpacerLength=0 -@@ -42,4 +42,4 @@ - # Use Vmatch [1] or internal tool [0] (default) - suffix.tool = 0 - # Vmatch path, if used nad not in path --suffix.path= -\ No newline at end of file -+suffix.path= ---- a/LogolExec.sh -+++ b/LogolExec.sh -@@ -21,5 +21,5 @@ - LOGOL_LOG4J=$LOGOL_HOME/log4j.properties - fi - --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:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$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.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 $* - ---- a/LogolMultiExec.sh -+++ b/LogolMultiExec.sh -@@ -25,5 +25,5 @@ - - echo "calling logol with parameters "$* - --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:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$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.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 $* - Copied: trunk/packages/logol/tags/1.7.0-1/debian/patches/setDebianDirs (from rev 16724, trunk/packages/logol/trunk/debian/patches/setDebianDirs) =================================================================== --- trunk/packages/logol/tags/1.7.0-1/debian/patches/setDebianDirs (rev 0) +++ trunk/packages/logol/tags/1.7.0-1/debian/patches/setDebianDirs 2014-04-18 13:19:24 UTC (rev 16728) @@ -0,0 +1,55 @@ +Subject: Use debian dirs for logs +Description: Debian policy hierarchy use +Author: Olivier Sallou <[email protected]> +Last-Updated: 2012-06-18 +--- a/log4j.properties ++++ b/log4j.properties +@@ -13,6 +13,6 @@ + + + log4j.appender.A2=org.apache.log4j.FileAppender +-log4j.appender.A2.File=/home/osallou/CODE/TEST/logol.log ++log4j.appender.A2.File=/var/log/logol/logol.log + log4j.appender.A2.layout=org.apache.log4j.PatternLayout +-log4j.appender.A2.layout.ConversionPattern=%d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - %m%n +\ No newline at end of file ++log4j.appender.A2.layout.ConversionPattern=%d{MM-dd@HH:mm:ss} %-5p (%13F:%L) %3x - %m%n +--- a/prolog/logol.properties ++++ b/prolog/logol.properties +@@ -11,9 +11,9 @@ + #maxMatchSize=30000 + maxMatchSize=0 + # Temporary directory used for the analysis. Should be local to the node +-workingDir=/tmp/Logol ++workingDir=/tmp/ + # Directory where to place the results. In case of cluster usage, result must be a shared directory between nodes +-dir.result=/tmp/Logol ++dir.result=/var/lib/logol/results/ + # Maximum length of a spacer when looking forward for a match + #maxSpacerLength=10000 + maxSpacerLength=0 +@@ -42,4 +42,4 @@ + # Use Cassiopee [2] (default) or Vmatch [1] or ruby cassiopee gem [0] + suffix.tool = 2 + # Vmatch path, if used nad not in path +-suffix.path= +\ No newline at end of file ++suffix.path= +--- a/LogolExec.sh ++++ b/LogolExec.sh +@@ -21,5 +21,5 @@ + LOGOL_LOG4J=$LOGOL_HOME/log4j.properties + fi + +-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:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$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.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 $* + +--- a/LogolMultiExec.sh ++++ b/LogolMultiExec.sh +@@ -25,5 +25,5 @@ + + echo "calling logol with parameters "$* + +-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:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$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.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 $* + _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
