[med-svn] r11410 - in trunk/packages/logol/trunk: . debian debian/patches debian/source
Olivier Sallou
osallou at alioth.debian.org
Thu Jun 21 09:40:40 UTC 2012
Author: osallou
Date: 2012-06-21 09:40:40 +0000 (Thu, 21 Jun 2012)
New Revision: 11410
Added:
trunk/packages/logol/trunk/debian/
trunk/packages/logol/trunk/debian/README.source
trunk/packages/logol/trunk/debian/changelog
trunk/packages/logol/trunk/debian/compat
trunk/packages/logol/trunk/debian/control
trunk/packages/logol/trunk/debian/copyright
trunk/packages/logol/trunk/debian/docs
trunk/packages/logol/trunk/debian/get-orig-source.sh
trunk/packages/logol/trunk/debian/logol-bin.dirs
trunk/packages/logol/trunk/debian/logol-bin.links
trunk/packages/logol/trunk/debian/logol-bin.lintian-overrides
trunk/packages/logol/trunk/debian/logol.dirs
trunk/packages/logol/trunk/debian/logol.doc-base
trunk/packages/logol/trunk/debian/logol.examples
trunk/packages/logol/trunk/debian/logol.install
trunk/packages/logol/trunk/debian/logol.links
trunk/packages/logol/trunk/debian/logol.lintian-overrides
trunk/packages/logol/trunk/debian/logol.manpages
trunk/packages/logol/trunk/debian/patches/
trunk/packages/logol/trunk/debian/patches/fixDrmmato6.2
trunk/packages/logol/trunk/debian/patches/fixLibPath
trunk/packages/logol/trunk/debian/patches/fix_doc_generation
trunk/packages/logol/trunk/debian/patches/series
trunk/packages/logol/trunk/debian/patches/setDebianDirs
trunk/packages/logol/trunk/debian/postinst
trunk/packages/logol/trunk/debian/rules
trunk/packages/logol/trunk/debian/source/
trunk/packages/logol/trunk/debian/source/format
trunk/packages/logol/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications (1.5.0-1) to trunk
Property changes on: trunk/packages/logol/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
+ 1
Added: trunk/packages/logol/trunk/debian/README.source
===================================================================
--- trunk/packages/logol/trunk/debian/README.source (rev 0)
+++ trunk/packages/logol/trunk/debian/README.source 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,6 @@
+Information for package Logol
+----------------------------
+
+ logol-grammar.pdf can be generated from Doc/grammar/generate.sh.
+
+ API for prolog code (needed for extra developments only) can be generated with tools/generate-doc.sh but requires swi-prolog latex library, not available for the moment in Debian repository. It requires swi-prolog source install.
Added: trunk/packages/logol/trunk/debian/changelog
===================================================================
--- trunk/packages/logol/trunk/debian/changelog (rev 0)
+++ trunk/packages/logol/trunk/debian/changelog 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,5 @@
+logol (1.5.0-1) unstable; urgency=low
+
+ * Initial release (Closes: #678373).
+
+ -- Olivier Sallou <osallou at debian.org> Thu, 21 Jun 2012 12:50:22 +0200
Added: trunk/packages/logol/trunk/debian/compat
===================================================================
--- trunk/packages/logol/trunk/debian/compat (rev 0)
+++ trunk/packages/logol/trunk/debian/compat 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1 @@
+8
Added: trunk/packages/logol/trunk/debian/control
===================================================================
--- trunk/packages/logol/trunk/debian/control (rev 0)
+++ trunk/packages/logol/trunk/debian/control 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,38 @@
+Source: logol
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Uploaders: Olivier Sallou <osallou at debian.org>
+DM-Upload-Allowed: yes
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/logol/trunk/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/logol/trunk/?rev=0&sc=0
+Build-Depends: debhelper (>= 8.0.0),openjdk-6-jdk|default-jdk|sun-java6-jdk,ant,ruby (>=1.8),rubygems, gawk, swi-prolog,
+ 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, tex4ht, libncursesw5-dev, ruby-cassiopee, ant-optional
+Standards-Version: 3.9.3
+Homepage: http://logol.genouest.org
+
+Package: logol
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, openjdk-6-jre|default-jre|sun-java6-jre, ruby (>=1.8),rubygems, 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, logol-bin
+Description: Pattern maching 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, libncursesw5
+Description: Pattern maching 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.
Added: trunk/packages/logol/trunk/debian/copyright
===================================================================
--- trunk/packages/logol/trunk/debian/copyright (rev 0)
+++ trunk/packages/logol/trunk/debian/copyright 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,506 @@
+Format: http://dep.debian.net/deps/dep5
+Upstream-Name: logol
+Source: https://gforge.inria.fr/projects/logolexec
+
+Files: Doc/pldoc.sty
+Copyright: 1985-2004 University of Amsterdam
+License: LGPL-2+
+ On Debian systems, you can find the GNU Lesser General Public License in
+ the file /usr/share/common-licenses/LGPL-2
+
+Files: *
+Copyright: 2011 Olivier Sallou <olivier.sallou at irisa.fr>
+License: CeCILL
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+ Version 2.0 dated 2006-09-05.
+
+Files: debian/*
+Copyright: 2011 Olivier Sallou <olivier.sallou at irisa.fr>
+License: GPL-2+
+ This package is free software; you can redistribute it and/or modify
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+ along with this program. If not, see <http://www.gnu.org/licenses/>
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
Added: trunk/packages/logol/trunk/debian/docs
===================================================================
--- trunk/packages/logol/trunk/debian/docs (rev 0)
+++ trunk/packages/logol/trunk/debian/docs 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,8 @@
+changelog
+README.txt
+prolog/SWI-README
+Doc/LogolGrammar.txt
+Doc/tutorial.pdf
+Doc/logol-usage.pdf
+# Not available, requires antlrworks for generation
+#Doc/logol-grammar.pdf
Added: trunk/packages/logol/trunk/debian/get-orig-source.sh
===================================================================
--- trunk/packages/logol/trunk/debian/get-orig-source.sh (rev 0)
+++ trunk/packages/logol/trunk/debian/get-orig-source.sh 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,41 @@
+#!/bin/bash
+
+set -e
+
+PKG=`dpkg-parsechangelog | awk '/^Source/ { print $2 }'`
+VERSION=`uscan --rename --verbose --force-download |
+ grep "Newest version on remote site is .* local version is .*" |
+ head -n 1 |
+ sed "s/Newest version on remote site is \([a-z0-9.]\+\),.*/\1/"`
+
+#VERSION=`dpkg-parsechangelog | awk '/^Version/ { print $2 }'| cut -d"-" -f1`
+#svn export svn://scm.gforge.inria.fr/svn/logolexec/trunk/LogolExec ${PKG}-${VERSION}.orig
+
+mkdir -p ../tarballs
+cd ../tarballs
+
+UTAR="${PKG}_${VERSION}.orig.tar.bz2"
+mv ../${UTAR} .
+tar xfj ${UTAR}
+
+mv ${PKG}-${VERSION} ${PKG}-${VERSION}.orig
+
+rm -rf ${PKG}-${VERSION}.orig/Doc/uml
+rm -f ${PKG}-${VERSION}.orig/Doc/Service*
+#mv ${PKG}-${VERSION}.orig/lib/antlrworks-1.4.2.jar .
+rm -rf ${PKG}-${VERSION}.orig/lib/*
+#mv antlrworks-1.4.2.jar ${PKG}-${VERSION}.orig/lib/
+rm -rf ${PKG}-${VERSION}.orig/Doc/JavaDoc
+chmod 755 ${PKG}-${VERSION}.orig/Doc/grammar/*.sh
+chmod 755 ${PKG}-${VERSION}.orig/tools/*.sh
+rm -f ${PKG}-${VERSION}.orig/Doc/*.mdr*
+rm -f ${PKG}-${VERSION}.orig/prolog/*.exe
+# Will be regenerated at build time
+rm -f ${PKG}-${VERSION}.orig/src/org/irisa/genouest/logol/parser/*
+# Will be rewritten from template
+rm -f ${PKG}-${VERSION}.orig/tools/suffixSearch.sh
+
+
+BZIP2="--best" tar -cjf ${PKG}_${VERSION}.orig.tar.bz2 ${PKG}-${VERSION}.orig
+
+rm -rf ${PKG}-${VERSION}.orig
Property changes on: trunk/packages/logol/trunk/debian/get-orig-source.sh
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/logol/trunk/debian/logol-bin.dirs
===================================================================
--- trunk/packages/logol/trunk/debian/logol-bin.dirs (rev 0)
+++ trunk/packages/logol/trunk/debian/logol-bin.dirs 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1 @@
+usr/lib/logol
Added: trunk/packages/logol/trunk/debian/logol-bin.links
===================================================================
--- trunk/packages/logol/trunk/debian/logol-bin.links (rev 0)
+++ trunk/packages/logol/trunk/debian/logol-bin.links 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,2 @@
+usr/lib/logol/logol.exe usr/share/logol/prolog/logol.exe
+usr/lib/logol/preanalyse.exe usr/share/logol/prolog/preanalyse.exe
Added: trunk/packages/logol/trunk/debian/logol-bin.lintian-overrides
===================================================================
--- trunk/packages/logol/trunk/debian/logol-bin.lintian-overrides (rev 0)
+++ trunk/packages/logol/trunk/debian/logol-bin.lintian-overrides 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,3 @@
+# Those executables are generated from Prolog code, stripping them prevent it from working
+logol-bin: unstripped-binary-or-object usr/lib/logol/preanalyse.exe
+logol-bin: unstripped-binary-or-object usr/lib/logol/logol.exe
Added: trunk/packages/logol/trunk/debian/logol.dirs
===================================================================
--- trunk/packages/logol/trunk/debian/logol.dirs (rev 0)
+++ trunk/packages/logol/trunk/debian/logol.dirs 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,4 @@
+etc/logol
+usr/share/logol
+var/log/logol
+var/lib/logol/results
Added: trunk/packages/logol/trunk/debian/logol.doc-base
===================================================================
--- trunk/packages/logol/trunk/debian/logol.doc-base (rev 0)
+++ trunk/packages/logol/trunk/debian/logol.doc-base 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,8 @@
+Document: logol
+Title: Logol User Manual
+Author: Olivier Sallou
+Abstract: Tutorial to build a grammar
+Section: Science/Biology
+
+Format: PDF
+Files: /usr/share/doc/logol/tutorial.pdf.gz
Added: trunk/packages/logol/trunk/debian/logol.examples
===================================================================
--- trunk/packages/logol/trunk/debian/logol.examples (rev 0)
+++ trunk/packages/logol/trunk/debian/logol.examples 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1 @@
+test/*
Added: trunk/packages/logol/trunk/debian/logol.install
===================================================================
--- trunk/packages/logol/trunk/debian/logol.install (rev 0)
+++ trunk/packages/logol/trunk/debian/logol.install 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,10 @@
+lib usr/share/logol/
+prolog usr/share/logol/
+tools usr/share/logol/
+convert2fasta.sh usr/share/logol/
+convert2gff.sh usr/share/logol/
+LogolExec.sh usr/share/logol/
+LogolMultiExec.sh usr/share/logol/
+Model2Grammar.sh usr/share/logol/
+log4j.properties usr/share/logol/
+
Added: trunk/packages/logol/trunk/debian/logol.links
===================================================================
--- trunk/packages/logol/trunk/debian/logol.links (rev 0)
+++ trunk/packages/logol/trunk/debian/logol.links 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,19 @@
+usr/share/logol/LogolMultiExec.sh usr/bin/LogolMultiExec
+usr/share/logol/LogolExec.sh usr/bin/LogolExec
+etc/logol/logol.properties usr/share/logol/prolog/logol.properties
+usr/share/java/biojava.jar usr/share/logol/lib/biojava.jar
+usr/share/java/activation.jar usr/share/logol/lib/activation.jar
+usr/share/java/bytecode.jar usr/share/logol/lib/bytecode.jar
+usr/share/java/drmaa.jar usr/share/logol/lib/drmaa.jar
+usr/share/java/antlr3-runtime.jar usr/share/logol/lib/antlr.jar
+usr/share/java/commons-cli.jar usr/share/logol/lib/commons-cli.jar
+usr/share/java/commons-lang.jar usr/share/logol/lib/commons-lang.jar
+usr/share/java/commons-collections3.jar usr/share/logol/lib/commons-collections.jar
+usr/share/java/commons-logging.jar usr/share/logol/lib/commons-logging.jar
+usr/share/java/commons-configuration.jar usr/share/logol/lib/commons-configuration.jar
+usr/share/java/xalan2.jar usr/share/logol/lib/xalan.jar
+usr/share/java/xercesImpl.jar usr/share/logol/lib/xercesImpl.jar
+usr/share/java/xml-apis.jar usr/share/logol/lib/xml-apis.jar
+usr/share/java/gnumail.jar usr/share/logol/lib/mail.jar
+usr/share/java/log4j-1.2.jar usr/share/logol/lib/log4j-1.2.jar
+usr/share/java/serializer.jar usr/share/logol/lib/serializer.jar
Added: trunk/packages/logol/trunk/debian/logol.lintian-overrides
===================================================================
--- trunk/packages/logol/trunk/debian/logol.lintian-overrides (rev 0)
+++ trunk/packages/logol/trunk/debian/logol.lintian-overrides 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,5 @@
+# This is a template, not used by upstream program
+logol: executable-not-elf-or-script usr/share/logol/tools/suffixSearchTpl.sh
+# Work directories required for examples to run
+logol: package-contains-empty-directory usr/share/doc/logol/examples/results/
+logol: package-contains-empty-directory usr/share/doc/logol/examples/tmp/
Added: trunk/packages/logol/trunk/debian/logol.manpages
===================================================================
--- trunk/packages/logol/trunk/debian/logol.manpages (rev 0)
+++ trunk/packages/logol/trunk/debian/logol.manpages 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,2 @@
+Doc/LogolExec.1
+Doc/LogolMultiExec.1
Added: trunk/packages/logol/trunk/debian/patches/fixDrmmato6.2
===================================================================
--- trunk/packages/logol/trunk/debian/patches/fixDrmmato6.2 (rev 0)
+++ trunk/packages/logol/trunk/debian/patches/fixDrmmato6.2 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,25 @@
+Subject: DRMAA API change between 6.1 and 6.2
+Description: Debian DRMAA is v6.2, API need an update
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 18/06/12
+--- a/src/org/irisa/genouest/logol/dispatcher/SGEJobManager.java
++++ b/src/org/irisa/genouest/logol/dispatcher/SGEJobManager.java
+@@ -10,6 +10,7 @@
+ import org.ggf.drmaa.Session;
+ import org.ggf.drmaa.SessionFactory;
+ import org.irisa.genouest.logol.Constants;
++import java.util.Arrays;
+
+ /*
+ * Manage the submission of jobs on a SGE system using DRMAA Java library.
+@@ -76,7 +77,9 @@
+ // Redirect DRM streams
+ jt.setOutputPath(":" + out+".out");
+ jt.setErrorPath(":" + out + ".err");
+- jt.setArgs(new String[] {arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)});
++ String[] tmpargs = new String[] {arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)};
++ jt.setArgs(Arrays.asList(tmpargs));
++ // DRMAA 6.1 jt.setArgs(new String[] {arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)});
+ jt.setRemoteCommand(installPath + System.getProperty(Constants.FILESEPARATORPROPERTY)+ "LogolExec.sh");
+ jobId = session.runJob(jt);
+ logger.info("Executing job: "+jobId);
Added: trunk/packages/logol/trunk/debian/patches/fixLibPath
===================================================================
--- trunk/packages/logol/trunk/debian/patches/fixLibPath (rev 0)
+++ trunk/packages/logol/trunk/debian/patches/fixLibPath 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,57 @@
+Subject: Use debian library for generation
+Description: Debian libraries should be used
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 18/06/12
+--- 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="dist">
+
+ <property environment="env" />
+
+@@ -50,6 +50,9 @@
+ <fileset dir="${basedir}/lib">
+ <patternset refid="java.libs" />
+ </fileset>
++ <fileset dir="/usr/share/java" >
++ <patternset refid="java.libs" />
++ </fileset>
+ </path>
+
+
+@@ -130,6 +133,25 @@
+ <fileset dir="${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" />
+@@ -189,6 +211,7 @@
+ <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>
Added: trunk/packages/logol/trunk/debian/patches/fix_doc_generation
===================================================================
--- trunk/packages/logol/trunk/debian/patches/fix_doc_generation (rev 0)
+++ trunk/packages/logol/trunk/debian/patches/fix_doc_generation 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,15 @@
+Subject: Use debian library for generation
+Description: Debian libraries should be used
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 18/06/12
+--- a/Doc/grammar/generate.sh
++++ b/Doc/grammar/generate.sh
+@@ -9,7 +9,7 @@
+
+ rm -rf $CURDIR/output
+ mkdir $CURDIR/output
+-java -cp $CURDIR/../../lib/antlrworks-1.4.2.jar org.antlr.works.Console -f $CURDIR/logol.tmp.g -o $CURDIR/output/ -sd eps -verbose
++java -cp /usr/share/java/antlr.jar org.antlr.works.Console -f $CURDIR/logol.tmp.g -o $CURDIR/output/ -sd eps -verbose
+
+ rm $CURDIR/logol.tmp.g
+
Added: trunk/packages/logol/trunk/debian/patches/series
===================================================================
--- trunk/packages/logol/trunk/debian/patches/series (rev 0)
+++ trunk/packages/logol/trunk/debian/patches/series 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,4 @@
+fixLibPath
+fixDrmmato6.2
+setDebianDirs
+fix_doc_generation
Added: trunk/packages/logol/trunk/debian/patches/setDebianDirs
===================================================================
--- trunk/packages/logol/trunk/debian/patches/setDebianDirs (rev 0)
+++ trunk/packages/logol/trunk/debian/patches/setDebianDirs 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,55 @@
+Subject: Use debian dirs for logs
+Description: Debian policy hierarchy use
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 18/06/12
+--- 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 at HH:mm:ss} %-5p (%13F:%L) %3x - %m%n
+\ No newline at end of file
++log4j.appender.A2.layout.ConversionPattern=%d{MM-dd at 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
+@@ -17,5 +17,5 @@
+
+ echo "calling logol with parameters "$*
+
+-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-1.4.2.jar org.irisa.genouest.logol.Logol $*
++java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_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:$LOGOL_HOME/lib/commons-configuration.jar:$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 $*
+
+--- a/LogolMultiExec.sh
++++ b/LogolMultiExec.sh
+@@ -20,5 +20,5 @@
+
+ echo "calling logol with parameters "$*
+
+-java -Xms512m -Xmx1024m -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_HOME/log4j.properties -classpath $LOGOL_HOME/lib/xalan.jar:$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_HOME/log4j.properties -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 $*
+
Added: trunk/packages/logol/trunk/debian/postinst
===================================================================
--- trunk/packages/logol/trunk/debian/postinst (rev 0)
+++ trunk/packages/logol/trunk/debian/postinst 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,40 @@
+#!/bin/sh
+# postinst script for logol
+#
+# see: dh_installdeb(1)
+
+set -e
+
+# summary of how this script can be called:
+# * <postinst> `configure' <most-recently-configured-version>
+# * <old-postinst> `abort-upgrade' <new version>
+# * <conflictor's-postinst> `abort-remove' `in-favour' <package>
+# <new-version>
+# * <postinst> `abort-remove'
+# * <deconfigured's-postinst> `abort-deconfigure' `in-favour'
+# <failed-install-package> <version> `removing'
+# <conflicting-package> <version>
+# for details, see http://www.debian.org/doc/debian-policy/ or
+# the debian-policy package
+
+
+case "$1" in
+ configure)
+ chmod -R 777 /var/lib/logol/results
+ ;;
+
+ abort-upgrade|abort-remove|abort-deconfigure)
+ ;;
+
+ *)
+ echo "postinst called with unknown argument \`$1'" >&2
+ exit 1
+ ;;
+esac
+
+# dh_installdeb will replace this with shell code automatically
+# generated by other debhelper scripts.
+
+#DEBHELPER#
+
+exit 0
Added: trunk/packages/logol/trunk/debian/rules
===================================================================
--- trunk/packages/logol/trunk/debian/rules (rev 0)
+++ trunk/packages/logol/trunk/debian/rules 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,46 @@
+#!/usr/bin/make -f
+# -*- makefile -*-
+
+# Uncomment this to turn on verbose mode.
+#export DH_VERBOSE=1
+
+DEB_ANT_BUILD_TARGET=create-jar,test_swi
+
+%:
+ dh $@
+
+override_dh_install:
+ dh_install
+ #touch debian/logol/var/log/logol/logol.log
+ #chmod 644 debian/logol/var/log/logol/logol.log
+ rm -f debian/logol/usr/share/logol/prolog/*.c
+ mv debian/logol/usr/share/logol/prolog/logol.exe debian/logol-bin/usr/lib/logol/
+ mv debian/logol/usr/share/logol/prolog/preanalyse.exe debian/logol-bin/usr/lib/logol/
+ mv debian/logol/usr/share/logol/prolog/logol.properties debian/logol/etc/logol/logol.properties
+ chmod 755 debian/logol/usr/share/logol/*.sh
+ chmod 755 debian/logol/usr/share/logol/tools/*.sh
+ chmod 755 debian/logol/usr/share/logol/tools/*.rb
+ #chmod 755 debian/logol/usr/share/logol/prolog/*.sh
+ chmod 755 debian/logol/usr/share/logol/tools/mycostfunction
+ # Not available, requires pldoc, not currently available in Debian SWI-Prolog
+ #cp Doc/logolParser.pdf debian/logol/usr/share/doc/logol/
+
+override_dh_clean:
+ dh_clean
+ rm -f Swi*.xml
+ rm -f prolog/*.exe
+ rm -f lib/*.jar
+ rm -f *.log
+ rm -f src/org/irisa/genouest/logol/parser/*
+ rm -f tools/suffixSearch.sh
+
+override_dh_installexamples:
+ rm -f test/tmp/*
+ rm -f test/results/*
+ dh_installexamples
+
+override_dh_strip:
+ dh_strip -Xlogol.exe -Xpreanalyse.exe
+
+get-orig-source:
+ debian/get-orig-source.sh
Property changes on: trunk/packages/logol/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
+ *
Added: trunk/packages/logol/trunk/debian/source/format
===================================================================
--- trunk/packages/logol/trunk/debian/source/format (rev 0)
+++ trunk/packages/logol/trunk/debian/source/format 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1 @@
+3.0 (quilt)
Added: trunk/packages/logol/trunk/debian/watch
===================================================================
--- trunk/packages/logol/trunk/debian/watch (rev 0)
+++ trunk/packages/logol/trunk/debian/watch 2012-06-21 09:40:40 UTC (rev 11410)
@@ -0,0 +1,2 @@
+version=3
+https://gforge.inria.fr/frs/?group_id=1318 .*/logol-(\d[\d.-]+)\.tar\.bz2
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