debian/0000755000000000000000000000000012320242062007157 5ustar debian/logol-bin.install0000644000000000000000000000010512275420075012440 0ustar prolog/logol.exe usr/lib/logol/ prolog/preanalyse.exe usr/lib/logol/ debian/logol.install0000644000000000000000000000046112275420075011677 0ustar 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/ prolog/logol.properties etc/logol/ debian/docs0000644000000000000000000000030012275420076010037 0ustar changelog README.txt prolog/SWI-README Doc/LogolGrammar.txt Doc/tutorial.pdf Doc/logol-usage.pdf Doc/logolParser.pdf # Not available, requires antlrworks for generation #Doc/logol-grammar.pdf debian/logol.doc-base0000644000000000000000000000027012275420076011705 0ustar 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 debian/copyright0000644000000000000000000005454412275420075011141 0ustar Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/ 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 License: CeCILL CeCILL FREE SOFTWARE LICENSE AGREEMENT . . 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No supplement or modification to the terms and conditions hereof shall be effective as between the Parties unless it is made in writing and signed by their duly authorized representatives. . 11.4 In the event that one or more of the provisions hereof were to conflict with a current or future applicable act or legislative text, said act or legislative text shall prevail, and the Parties shall make the necessary amendments so as to comply with said act or legislative text. All other provisions shall remain effective. Similarly, invalidity of a provision of the Agreement, for any reason whatsoever, shall not cause the Agreement as a whole to be invalid. . 11.5 LANGUAGE . The Agreement is drafted in both French and English and both versions are deemed authentic. . Article 12 - NEW VERSIONS OF THE AGREEMENT . 12.1 Any person is authorized to duplicate and distribute copies of this Agreement. . 12.2 So as to ensure coherence, the wording of this Agreement is protected and may only be modified by the authors of the License, who reserve the right to periodically publish updates or new versions of the Agreement, each with a separate number. These subsequent versions may address new issues encountered by Free Software. . 12.3 Any Software distributed under a given version of the Agreement may only be subsequently distributed under the same version of the Agreement or a subsequent version, subject to the provisions of Article 5.3.4. . Article 13 - GOVERNING LAW AND JURISDICTION . 13.1 The Agreement is governed by French law. The Parties agree to endeavor to seek an amicable solution to any disagreements or disputes that may arise during the performance of the Agreement. . 13.2 Failing an amicable solution within two (2) months as from their occurrence, and unless emergency proceedings are necessary, the disagreements or disputes shall be referred to the Paris Courts having jurisdiction, by the more diligent Party. . Version 2.0 dated 2006-09-05. Files: debian/* Copyright: 2011 Olivier Sallou License: GPL-2+ This package is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. . This package is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. . You should have received a copy of the GNU General Public License along with this program. If not, see . On Debian systems, the complete text of the GNU General Public License version 2 can be found in "/usr/share/common-licenses/GPL-2". debian/logol.lintian-overrides0000644000000000000000000000031012275420075013660 0ustar # 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/ debian/changelog0000644000000000000000000000756512320242043011045 0ustar logol (1.6.10-1build1) trusty; urgency=medium * No-change rebuild to update swi-prolog dependency. -- Matthias Klose Sun, 06 Apr 2014 13:58:06 +0200 logol (1.6.10-1) unstable; urgency=low * New upstream release, fix bug on Hamming error search -- Olivier Sallou 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 (Closes: #735579). * Upgrade to Standards 3.9.5. -- Olivier Sallou Fri, 17 Jan 2014 09:07:38 +0100 logol (1.6.9-2) unstable; urgency=low * Fix prolog doc generation (Closes: #730916). -- Olivier Sallou 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 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 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 Fri, 25 Oct 2013 13:48:22 +0200 logol (1.6.4-1) unstable; urgency=low * New upstream release fixing bugs -- Olivier Sallou 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 Mon, 02 Sep 2013 08:54:46 +0200 logol (1.6.2-3) unstable; urgency=low * Fix swi-prolog compilation (Closes: #719030). -- Olivier Sallou 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 Mon, 03 Jun 2013 23:36:49 +0100 logol (1.6.2-1) unstable; urgency=low * New upstream release (bug fixes) -- Olivier Sallou Fri, 24 May 2013 14:37:24 +0200 logol (1.6.1-1) unstable; urgency=low * New upstream release (bug fixes) -- Olivier Sallou Tue, 09 Apr 2013 16:57:33 +0200 logol (1.6.0-1) unstable; urgency=low * New upstream release with bug fixes -- Olivier Sallou 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 -- Olivier Sallou 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 james.page@ubuntu.com (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 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 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 Sun, 01 Jul 2012 23:49:16 +0200 logol (1.5.0-1) unstable; urgency=low * Initial release (Closes: #678373). -- Olivier Sallou Thu, 21 Jun 2012 12:50:22 +0200 debian/logol.links0000644000000000000000000000231212275420076011347 0ustar 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 debian/logol-bin.dirs0000644000000000000000000000001612275420075011734 0ustar usr/lib/logol debian/compat0000644000000000000000000000000212275420075010370 0ustar 8 debian/logol.examples0000644000000000000000000000000712275420076012044 0ustar test/* debian/logol.dirs0000644000000000000000000000007612275420075011174 0ustar etc/logol usr/share/logol var/log/logol var/lib/logol/results debian/patches/0000755000000000000000000000000012275420643010622 5ustar debian/patches/harden_swipl_declarations0000644000000000000000000001005212275420075015751 0ustar Author: Olivier Sallou Subject: swi-prolog raise error instead of warnings for undefined modules Description: swi-prolog raise an error for exported procedure not matching declared procedure. It also raises error on modules declared for sicstus prolog. Patch need to remove them (not needed for swi-prolog) Forwarded: yes Bug: https://gforge.inria.fr/tracker/index.php?func=detail&aid=16249&group_id=1318&atid=5219 --- a/prolog/logol.pl +++ b/prolog/logol.pl @@ -1,4 +1,4 @@ -:- module(logol,[writeFinalMatches/0,isMin/5,replaceMatch/4,appendMatch/3,getCounter/1,config/1,optimalmatch/5,matchstore/2,isMax/3,parseResults/2,checkAlphabetPercentage/3,mapListExact/2,mapListGlobal/2,mapListLocal/2,mapListLocal0/2,matchExist/2,mapModels/3,externalinterfacewithspacer/2,externalinterface/2,notpred_pos/6,between/3,notexact_pos/6,notexact/3,matchExist/1,mapModels/2,mapList/2,mydb/1,matchlist/2,isexactwithgaponly/5,isexactwithgaponly_pos/5,setParent/2,getParent/2,logData/2,logolMain/5,cut_sequence/3,isequal/2,isexact_pos/4,isexactwithgapanderror_pos/5,isexactwitherroronly_pos/5,spacer_withresult_pos/5,wordSize_pos/4,getPosition_pos/3,wordContent_pos/4,checkPosition_pos/4,anySpacer_pos/7,repeatPredicate_pos/14,testOverlap_pos/5,getsuffixmatch_pos/12,getWordContent/4,openSequenceStream/1,closeSequenceStream/0,getCharsFromPosition/3,getNChar/3,resetParamList/3,getKnownVariables/2,getPosition/3,myCost/4,getDistance/3,initResultFile/1,closeResultFile/1,getParentVariable/2,is4me/5,outputfile/1,writeallresult/2,maxsize/1,getresult/2,offset/1,setSequence/2,computeCost/2,getsuffixmatch/12,writeSequence/2,sequenceData/3,suffixmatch/9,repeatPredicate/14,anySpacer/5,anySpacer/7,any/2,isoverlap/5,morphism/3,spacer_withresult/5,isexact/3,isexact/4,isexact/5,isexactwithgapanderror/4,isexactwithgapanderror/5,isexactwitherroronly/4,isexactwitherroronly/5,matrix/3, iscompequal/2,getcomplement/2,getreversecomplement/2,applymorphism/4, checkCost/4,cost/4,parentalCost/4,varDefinition/5,saveVariable/7,saveVariableByRef/7,saveVariable/8,getVariable/9,removeVariable/1,wordSize/3,wordSize/4,percent/3,percent2int/3,checkCost/4,checkCost/5,checkPosition/3,checkPosition/5,checkRelativePosition/4,getContent/3,getContent/4,pushResult/2],[assertions,basicmodes,functions,regtypes,hiord]). +:- module(logol,[writeFinalMatches/0,isMin/5,replaceMatch/4,appendMatch/3,getCounter/1,config/1,optimalmatch/5,matchstore/2,isMax/3,parseResults/2,checkAlphabetPercentage/3,mapListExact/2,mapListGlobal/2,mapListLocal/2,mapListLocal0/2,matchExist/2,mapModels/3,externalinterfacewithspacer/2,externalinterface/2,notpred_pos/6,between/3,notexact_pos/6,notexact/3,matchExist/1,mapModels/2,mapList/2,mydb/1,matchlist/2,isexactwithgaponly/5,isexactwithgaponly_pos/5,setParent/2,getParent/2,logData/2,logolMain/5,cut_sequence/3,isequal/2,isexact_pos/4,isexactwithgapanderror_pos/5,isexactwitherroronly_pos/5,spacer_withresult_pos/5,wordSize_pos/4,getPosition_pos/2,wordContent_pos/4,checkPosition_pos/4,anySpacer_pos/7,repeatPredicate_pos/14,testOverlap_pos/5,getsuffixmatch_pos/12,getWordContent/4,openSequenceStream/2,closeSequenceStream/0,getCharsFromPosition/3,getNChar/3,resetParamList/3,getKnownVariables/2,getPosition/3,myCost/4,getDistance/3,initResultFile/1,closeResultFile/1,getParentVariable/2,is4me/5,outputfile/1,writeallresult/2,maxsize/1,getresult/2,offset/1,setSequence/2,computeCost/2,getsuffixmatch/12,writeSequence/2,sequenceData/3,suffixmatch/9,repeatPredicate/14,anySpacer/5,anySpacer/7,any/2,isoverlap/5,morphism/3,spacer_withresult/5,isexact/3,isexact/4,isexact/5,isexactwithgapanderror/4,isexactwithgapanderror/5,isexactwitherroronly/4,isexactwitherroronly/5,matrix/3, iscompequal/2,getcomplement/2,getreversecomplement/2,applymorphism/4, checkCost/4,cost/4,parentalCost/4,varDefinition/5,saveVariable/8,saveVariable/9,getVariable/9,removeVariable/1,wordSize/3,wordSize/4,percent/3,percent2int/3,checkCost/4,checkCost/5,checkPosition/3,checkPosition/5,checkRelativePosition/4,getContent/3,getContent/4,pushResult/2,countAlphabet/4,isexactwithdistinctgapanderror_pos/7],[]). /** Logol Prolog API debian/patches/fix_doc_generation0000644000000000000000000000105712275420075014375 0ustar Subject: Use debian library for generation Description: Debian libraries should be used Author: Olivier Sallou Last-Updated: 2012-06-18 --- 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 debian/patches/remove_rubygems_usage0000644000000000000000000000235412275420575015153 0ustar Subject: Remove explicit use of rubygems Description: Supported version of Ruby in Jessie+ are higher that 1.9 and they all automatically load rubygems Author: Cédric Boutillier Last-Update: 2014-01-16 --- a/tools/logolIndex.rb +++ b/tools/logolIndex.rb @@ -1,5 +1,4 @@ #!/usr/bin/env ruby -require 'rubygems' require 'optparse' require 'logger' require 'cassiopee-mt' --- a/tools/logolSearch.rb +++ b/tools/logolSearch.rb @@ -22,9 +22,9 @@ DIR=File.expand_path(File.dirname(__FILE__)) if muteOnly.to_i == 1 - cmd = "ruby -rubygems "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError+" --hamming" + cmd = "ruby "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError+" --hamming" else - cmd = "ruby -rubygems "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError + cmd = "ruby "+DIR+"/logolIndex.rb --search "+sequence+".index --min "+minStart+" --max "+maxStart+" --pattern "+motifFileName+" --error "+nbError end Open3.popen3(cmd) do |stdin,stdout,stderr, wait_thr| debian/patches/setDebianDirs0000644000000000000000000001045612275420075013272 0ustar Subject: Use debian dirs for logs Description: Debian policy hierarchy use Author: Olivier Sallou 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 $* debian/patches/fixLibPath0000644000000000000000000000610412275420075012577 0ustar Subject: Use debian library for generation Description: Debian libraries should be used Author: Olivier Sallou Last-Updated: 2012-06-18 --- a/build.xml +++ b/build.xml @@ -1,5 +1,5 @@ - + @@ -57,6 +57,9 @@ + + + @@ -141,6 +144,25 @@ + + + + + + + + + + + + + + + + + + + @@ -200,6 +222,7 @@ + debian/patches/fix_pldoc2tex_generation0000644000000000000000000000136212275420075015533 0ustar Subject: generated tex by pldoc not supported by texlive Description: lpdoc generate tex file from prolog. Generated file fails to be converted with pdflatex since later releases. This patch modifies generated file to support pdf conversion. Author: Olivier Sallou Last-Updated: 2013-08-08 Forwarded: yes Bug: 719079 --- a/tools/generate-doc.sh +++ b/tools/generate-doc.sh @@ -2,6 +2,10 @@ sed 's/,\[assertions,basicmodes,functions,regtypes,hiord\]//' ../prolog/logol.pl > logoldoc.pl swipl -f swidoc.pl -- logoldoc.pl + +sed -i 's/makeindex/makeindex\n\\newenvironment{arguments}{\\textbf{Arguments} \\newline}{\\vspace*{0.5\\baselineskip}}/' logol.tex +sed -i 's/} &/}/g' logol.tex + pdflatex logol.tex rm logoldoc.pl debian/patches/fixDrmmato6.20000644000000000000000000000327412275420075013112 0ustar Subject: DRMAA API change between 6.1 and 6.2 Description: Debian DRMAA is v6.2, API need an update Author: Olivier Sallou Last-Updated: 2012-06-18 Forwarded: no --- 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. @@ -80,11 +81,16 @@ jt.setOutputPath(":" + out+".out"); jt.setErrorPath(":" + out + ".err"); if(OS.startsWith("win")) { - jt.setArgs(new String[] {installPath + System.getProperty(Constants.FILESEPARATORPROPERTY)+ "LogolExec.rb", arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)}); + //jt.setArgs(new String[] {installPath + System.getProperty(Constants.FILESEPARATORPROPERTY)+ "LogolExec.rb", 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)); jt.setRemoteCommand("ruby"); } else { - jt.setArgs(new String[] {arguments,jobsArgs.get(i)," -output "+jobsOutput.get(i)}); + //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)); + jt.setRemoteCommand(installPath + System.getProperty(Constants.FILESEPARATORPROPERTY)+ "LogolExec.sh"); } jobId = session.runJob(jt); debian/patches/fix_pldoc0000644000000000000000000000112512275420075012512 0ustar Subject: adapt to new swi-prolog Description: swipl doc generation changed and breaks current definition Author: Olivier Sallou Last-Updated: 2013-12-01 Forwarded: yes Bug: 739916 Upstream-Bug: https://gforge.inria.fr/tracker/index.php?func=detail&aid=16708&group_id=1318&atid=5219 --- a/tools/swidoc.pl +++ b/tools/swidoc.pl @@ -1,4 +1,4 @@ :- use_module(library(doc_latex)). -:- current_prolog_flag(argv,[_,_,_,_,Doc]),open('logol.tex',write,OS),latex_for_file(Doc,OS,[]),close(OS). +:- open('logol.tex',write,OS),latex_for_file('logoldoc.pl',OS,[]),close(OS). :-halt. debian/patches/fix_swipl_module_declaration0000644000000000000000000000763612275420075016476 0ustar Subject: fix module declaration for swipl, different from sicstus-prolog. Description: for swipl, default used in packaging, the module declaration is different. This patch fix this difference. Upstream manage both Forwarded: No Author: Olivier Sallou Last-Updated: 2013-10-07 --- a/prolog/logol.pl +++ b/prolog/logol.pl @@ -1,4 +1,4 @@ -:- module(logol,[writeFinalMatches/0,isMin/5,replaceMatch/4,appendMatch/3,getCounter/1,config/1,optimalmatch/5,matchstore/2,isMax/3,parseResults/2,checkAlphabetPercentage/3,mapListExact/2,mapListGlobal/2,mapListLocal/2,mapListLocal0/2,matchExist/2,mapModels/3,externalinterfacewithspacer/2,externalinterface/2,notpred_pos/6,between/3,notexact_pos/6,notexact/3,matchExist/1,mapModels/2,mapList/2,mydb/1,matchlist/2,isexactwithgaponly/5,isexactwithgaponly_pos/5,setParent/2,getParent/2,logData/2,logolMain/5,cut_sequence/3,isequal/2,isexact_pos/4,isexactwithgapanderror_pos/5,isexactwitherroronly_pos/5,spacer_withresult_pos/5,wordSize_pos/4,getPosition_pos/3,wordContent_pos/4,checkPosition_pos/4,anySpacer_pos/7,repeatPredicate_pos/14,testOverlap_pos/5,getsuffixmatch_pos/12,getWordContent/4,openSequenceStream/2,closeSequenceStream/0,getCharsFromPosition/3,getNChar/3,resetParamList/3,getKnownVariables/2,getPosition/3,myCost/4,getDistance/3,initResultFile/1,closeResultFile/1,getParentVariable/2,is4me/5,outputfile/1,writeallresult/2,maxsize/1,getresult/2,offset/1,setSequence/2,computeCost/2,getsuffixmatch/12,writeSequence/2,sequenceData/3,suffixmatch/9,repeatPredicate/14,anySpacer/5,anySpacer/7,any/2,isoverlap/5,morphism/3,spacer_withresult/5,isexact/3,isexact/4,isexact/5,isexactwithgapanderror/4,isexactwithgapanderror/5,isexactwitherroronly/4,isexactwitherroronly/5,matrix/3, iscompequal/2,getcomplement/2,getreversecomplement/2,applymorphism/4, checkCost/4,cost/4,parentalCost/4,varDefinition/5,saveVariable/8,getVariable/9,removeVariable/1,wordSize/3,wordSize/4,percent/3,percent2int/3,checkCost/4,checkCost/5,checkPosition/3,checkPosition/5,checkRelativePosition/4,getContent/3,getContent/4,pushResult/2,countAlphabet/4,isexactwithdistinctgapanderror_pos/7],[assertions,basicmodes,functions,regtypes,hiord]). +:- module(logol,[writeFinalMatches/0,isMin/5,replaceMatch/4,appendMatch/3,getCounter/1,config/1,optimalmatch/5,matchstore/2,isMax/3,parseResults/2,checkAlphabetPercentage/3,mapListExact/2,mapListGlobal/2,mapListLocal/2,mapListLocal0/2,matchExist/2,mapModels/3,externalinterfacewithspacer/2,externalinterface/2,notpred_pos/6,between/3,notexact_pos/6,notexact/3,matchExist/1,mapModels/2,mapList/2,mydb/1,matchlist/2,isexactwithgaponly/5,isexactwithgaponly_pos/5,setParent/2,getParent/2,logData/2,logolMain/5,cut_sequence/3,isequal/2,isexact_pos/4,isexactwithgapanderror_pos/5,isexactwitherroronly_pos/5,spacer_withresult_pos/5,wordSize_pos/4,getPosition_pos/3,wordContent_pos/4,checkPosition_pos/4,anySpacer_pos/7,repeatPredicate_pos/14,testOverlap_pos/5,getsuffixmatch_pos/12,getWordContent/4,openSequenceStream/2,closeSequenceStream/0,getCharsFromPosition/3,getNChar/3,resetParamList/3,getKnownVariables/2,getPosition/3,myCost/4,getDistance/3,initResultFile/1,closeResultFile/1,getParentVariable/2,is4me/5,outputfile/1,writeallresult/2,maxsize/1,getresult/2,offset/1,setSequence/2,computeCost/2,getsuffixmatch/12,writeSequence/2,sequenceData/3,suffixmatch/9,repeatPredicate/14,anySpacer/5,anySpacer/7,any/2,isoverlap/5,morphism/3,spacer_withresult/5,isexact/3,isexact/4,isexact/5,isexactwithgapanderror/4,isexactwithgapanderror/5,isexactwitherroronly/4,isexactwitherroronly/5,matrix/3, iscompequal/2,getcomplement/2,getreversecomplement/2,applymorphism/4, checkCost/4,cost/4,parentalCost/4,varDefinition/5,saveVariable/8,getVariable/9,removeVariable/1,wordSize/3,wordSize/4,percent/3,percent2int/3,checkCost/4,checkCost/5,checkPosition/3,checkPosition/5,checkRelativePosition/4,getContent/3,getContent/4,pushResult/2,countAlphabet/4,isexactwithdistinctgapanderror_pos/7],[]). /** Logol Prolog API debian/patches/series0000644000000000000000000000012012275420530012023 0ustar fixLibPath fixDrmmato6.2 setDebianDirs fix_doc_generation remove_rubygems_usage debian/get-orig-source.sh0000755000000000000000000000251112275420075012543 0ustar #!/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 debian/control0000644000000000000000000000400212275420075010571 0ustar Source: logol Section: science Priority: optional Maintainer: Debian Med Packaging Team Uploaders: Olivier Sallou 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. debian/rules0000755000000000000000000000260112275420076010252 0ustar #!/usr/bin/make -f # -*- makefile -*- # Uncomment this to turn on verbose mode. #export DH_VERBOSE=1 DEB_ANT_BUILD_TARGET=create-jar,test_swi DEB_ANT_ARGS=-Dant.build.javac.source=1.5 -Dant.build.javac.target=1.5 %: dh $@ override_dh_auto_build: mv tools/pldoc.sty tools/pldoc.sty.upstream dh_auto_build -- $(DEB_ANT_ARGS) ant -f build.xml doc override_dh_install: dh_install rm -f debian/logol/usr/share/logol/prolog/*.c rm -f debian/logol/usr/share/logol/prolog/*.exe rm -f debian/logol/usr/share/logol/prolog/logol.properties rm -f debian/logol/usr/share/logol/tools/*.keep_old_script if [ -e debian/logol ]; then chmod -f 755 debian/logol/usr/share/logol/*.sh; fi if [ -e debian/logol ]; then chmod -f 755 debian/logol/usr/share/logol/tools/*.sh; fi if [ -e debian/logol ]; then chmod -f 755 debian/logol/usr/share/logol/tools/*.rb; fi if [ -e debian/logol ]; then chmod -f 755 debian/logol/usr/share/logol/tools/mycostfunction; fi override_dh_clean: if [ -e tools/pldoc.sty.upstream ]; then mv tools/pldoc.sty.upstream tools/pldoc.sty; fi 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 debian/source/0000755000000000000000000000000012275420643010473 5ustar debian/source/format0000644000000000000000000000001412275420072011675 0ustar 3.0 (quilt) debian/README.source0000644000000000000000000000054612275420076011357 0ustar 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. debian/logol-bin.links0000644000000000000000000000017412275420075012120 0ustar usr/lib/logol/logol.exe usr/share/logol/prolog/logol.exe usr/lib/logol/preanalyse.exe usr/share/logol/prolog/preanalyse.exe debian/logol-bin.lintian-overrides0000644000000000000000000000033612275420075014436 0ustar # 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 debian/watch0000644000000000000000000000013312275420075010220 0ustar version=3 https://gforge.inria.fr/frs/?group_id=1318 .*/logol_(\d[\d.-]+)\.orig\.tar\.bz2 debian/logol.manpages0000644000000000000000000000004512275420075012022 0ustar Doc/LogolExec.1 Doc/LogolMultiExec.1