[med-svn] r19034 - in trunk/packages/logol/tags: . 1.7.2-1/debian 1.7.2-1/debian/patches
Olivier Sallou
osallou at moszumanska.debian.org
Wed Apr 8 15:19:40 UTC 2015
Author: osallou
Date: 2015-04-08 15:19:40 +0000 (Wed, 08 Apr 2015)
New Revision: 19034
Added:
trunk/packages/logol/tags/1.7.2-1/
trunk/packages/logol/tags/1.7.2-1/debian/README.Debian
trunk/packages/logol/tags/1.7.2-1/debian/changelog
trunk/packages/logol/tags/1.7.2-1/debian/control
trunk/packages/logol/tags/1.7.2-1/debian/get-orig-source.sh
trunk/packages/logol/tags/1.7.2-1/debian/patches/remove_drmaa_support
trunk/packages/logol/tags/1.7.2-1/debian/patches/series
trunk/packages/logol/tags/1.7.2-1/debian/patches/setDebianDirs
Removed:
trunk/packages/logol/tags/1.7.2-1/debian/changelog
trunk/packages/logol/tags/1.7.2-1/debian/control
trunk/packages/logol/tags/1.7.2-1/debian/get-orig-source.sh
trunk/packages/logol/tags/1.7.2-1/debian/patches/series
trunk/packages/logol/tags/1.7.2-1/debian/patches/setDebianDirs
Log:
[svn-buildpackage] Tagging logol 1.7.2-1
Copied: trunk/packages/logol/tags/1.7.2-1/debian/README.Debian (from rev 18738, trunk/packages/logol/trunk/debian/README.Debian)
===================================================================
--- trunk/packages/logol/tags/1.7.2-1/debian/README.Debian (rev 0)
+++ trunk/packages/logol/tags/1.7.2-1/debian/README.Debian 2015-04-08 15:19:40 UTC (rev 19034)
@@ -0,0 +1,5 @@
+Current release in Debian has removed DRMAA support due to gridengine removal of Jessie.
+
+When libdrmma-java is reintroduced, drmaa support will be set back in logol.
+
+This release will work in local mode only.
Deleted: trunk/packages/logol/tags/1.7.2-1/debian/changelog
===================================================================
--- trunk/packages/logol/trunk/debian/changelog 2015-01-31 23:32:16 UTC (rev 18701)
+++ trunk/packages/logol/tags/1.7.2-1/debian/changelog 2015-04-08 15:19:40 UTC (rev 19034)
@@ -1,132 +0,0 @@
-logol (1.7.0-1) unstable; urgency=low
-
- * New upstream release
-
- -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> 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 <boutil at debian.org> (Closes: #735579).
- * Upgrade to Standards 3.9.5.
-
- -- Olivier Sallou <osallou at debian.org> Fri, 17 Jan 2014 09:07:38 +0100
-
-logol (1.6.9-2) unstable; urgency=low
-
- * Fix prolog doc generation (Closes: #730916).
-
- -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> Fri, 25 Oct 2013 13:48:22 +0200
-
-logol (1.6.4-1) unstable; urgency=low
-
- * New upstream release fixing bugs
-
- -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> Mon, 02 Sep 2013 08:54:46 +0200
-
-logol (1.6.2-3) unstable; urgency=low
-
- * Fix swi-prolog compilation (Closes: #719030).
-
- -- Olivier Sallou <osallou at debian.org> 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 <dmitrij.ledkov at ubuntu.com> Mon, 03 Jun 2013 23:36:49 +0100
-
-logol (1.6.2-1) unstable; urgency=low
-
- * New upstream release (bug fixes)
-
- -- Olivier Sallou <osallou at debian.org> Fri, 24 May 2013 14:37:24 +0200
-
-logol (1.6.1-1) unstable; urgency=low
-
- * New upstream release (bug fixes)
-
- -- Olivier Sallou <osallou at debian.org> Tue, 09 Apr 2013 16:57:33 +0200
-
-logol (1.6.0-1) unstable; urgency=low
-
- * New upstream release with bug fixes
-
- -- Olivier Sallou <osallou at debian.org> 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 <erik.esterer at gmail.com>
-
- -- Olivier Sallou <osallou at debian.org> 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 at 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 <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> Sun, 01 Jul 2012 23:49:16 +0200
-
-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
Copied: trunk/packages/logol/tags/1.7.2-1/debian/changelog (from rev 19033, trunk/packages/logol/trunk/debian/changelog)
===================================================================
--- trunk/packages/logol/tags/1.7.2-1/debian/changelog (rev 0)
+++ trunk/packages/logol/tags/1.7.2-1/debian/changelog 2015-04-08 15:19:40 UTC (rev 19034)
@@ -0,0 +1,156 @@
+logol (1.7.2-1) unstable; urgency=medium
+
+ * New upstream release
+ d/control: use Standars 3.9.6
+
+ -- Olivier Sallou <osallou at debian.org> Thu, 05 Feb 2015 15:32:25 +0100
+
+logol (1.7.0-2) unstable; urgency=medium
+
+ * d/control,d/patches/remove_drmaa_support: Remove libdrmaa-java dependency
+ due to gridengine removal from Jessie (#776131).
+ d/series: remove drmaa patch
+ d/README.Debian: explain non drmaa support of this release
+
+ -- Olivier Sallou <osallou at debian.org> Sun, 01 Feb 2015 08:56:52 +0100
+
+logol (1.7.0-1.1) unstable; urgency=high
+
+ * Non-maintainer upload.
+ * No source changes, rebuild against swi-prolog 6.6.5
+ * Urgency high to not hold migration of swi-prolog for much longer
+
+ -- Євгеній Мещеряков <eugen at debian.org> Wed, 21 May 2014 21:26:00 +0200
+
+logol (1.7.0-1) unstable; urgency=low
+
+ * New upstream release
+
+ -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> 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 <boutil at debian.org> (Closes: #735579).
+ * Upgrade to Standards 3.9.5.
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 17 Jan 2014 09:07:38 +0100
+
+logol (1.6.9-2) unstable; urgency=low
+
+ * Fix prolog doc generation (Closes: #730916).
+
+ -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> Fri, 25 Oct 2013 13:48:22 +0200
+
+logol (1.6.4-1) unstable; urgency=low
+
+ * New upstream release fixing bugs
+
+ -- Olivier Sallou <osallou at debian.org> 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 <osallou at debian.org> Mon, 02 Sep 2013 08:54:46 +0200
+
+logol (1.6.2-3) unstable; urgency=low
+
+ * Fix swi-prolog compilation (Closes: #719030).
+
+ -- Olivier Sallou <osallou at debian.org> 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 <dmitrij.ledkov at ubuntu.com> Mon, 03 Jun 2013 23:36:49 +0100
+
+logol (1.6.2-1) unstable; urgency=low
+
+ * New upstream release (bug fixes)
+
+ -- Olivier Sallou <osallou at debian.org> Fri, 24 May 2013 14:37:24 +0200
+
+logol (1.6.1-1) unstable; urgency=low
+
+ * New upstream release (bug fixes)
+
+ -- Olivier Sallou <osallou at debian.org> Tue, 09 Apr 2013 16:57:33 +0200
+
+logol (1.6.0-1) unstable; urgency=low
+
+ * New upstream release with bug fixes
+
+ -- Olivier Sallou <osallou at debian.org> 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 <erik.esterer at gmail.com>
+
+ -- Olivier Sallou <osallou at debian.org> 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 at 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 <osallou at debian.org> 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 <osallou at debian.org> 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 <osallou at debian.org> Sun, 01 Jul 2012 23:49:16 +0200
+
+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
Deleted: trunk/packages/logol/tags/1.7.2-1/debian/control
===================================================================
--- trunk/packages/logol/trunk/debian/control 2015-01-31 23:32:16 UTC (rev 18701)
+++ trunk/packages/logol/tags/1.7.2-1/debian/control 2015-04-08 15:19:40 UTC (rev 19034)
@@ -1,46 +0,0 @@
-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>
-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.
Copied: trunk/packages/logol/tags/1.7.2-1/debian/control (from rev 19033, trunk/packages/logol/trunk/debian/control)
===================================================================
--- trunk/packages/logol/tags/1.7.2-1/debian/control (rev 0)
+++ trunk/packages/logol/tags/1.7.2-1/debian/control 2015-04-08 15:19:40 UTC (rev 19034)
@@ -0,0 +1,48 @@
+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>
+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, 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
+#libdrmaa-java removed from Jessie, to be reintroduced.
+Standards-Version: 3.9.6
+Homepage: http://logol.genouest.org
+
+Package: logol
+Architecture: all
+Depends: ${shlibs:Depends}, ${misc:Depends}, default-jre | java7-runtime,
+ ruby, gawk,
+ libbiojava-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
+#libdrmaa-java removed from Jessie, to be reintroduced.
+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/1.7.2-1/debian/get-orig-source.sh
===================================================================
--- trunk/packages/logol/trunk/debian/get-orig-source.sh 2015-01-31 23:32:16 UTC (rev 18701)
+++ trunk/packages/logol/tags/1.7.2-1/debian/get-orig-source.sh 2015-04-08 15:19:40 UTC (rev 19034)
@@ -1,41 +0,0 @@
-#!/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
Copied: trunk/packages/logol/tags/1.7.2-1/debian/get-orig-source.sh (from rev 19032, trunk/packages/logol/trunk/debian/get-orig-source.sh)
===================================================================
--- trunk/packages/logol/tags/1.7.2-1/debian/get-orig-source.sh (rev 0)
+++ trunk/packages/logol/tags/1.7.2-1/debian/get-orig-source.sh 2015-04-08 15:19:40 UTC (rev 19034)
@@ -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.xz"
+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
Copied: trunk/packages/logol/tags/1.7.2-1/debian/patches/remove_drmaa_support (from rev 18738, trunk/packages/logol/trunk/debian/patches/remove_drmaa_support)
===================================================================
--- trunk/packages/logol/tags/1.7.2-1/debian/patches/remove_drmaa_support (rev 0)
+++ trunk/packages/logol/tags/1.7.2-1/debian/patches/remove_drmaa_support 2015-04-08 15:19:40 UTC (rev 19034)
@@ -0,0 +1,166 @@
+Subject: libdrmaa-java removed from Debian (gridengine)
+Description: DRMAA job submission needs a Java drmaa library.
+ libdrmaa-java has been removed from Debian, bug: 776131.
+ This patch removes DRMAA related code waiting for library
+ reintroduction.
+ Logol will work on local mode only.
+Author: Olivier Sallou <osallou at debian.org>
+Last-Updated: 2015-02-01
+--- a/src/org/irisa/genouest/logol/dispatcher/Dispatch.java
++++ b/src/org/irisa/genouest/logol/dispatcher/Dispatch.java
+@@ -230,7 +230,6 @@
+ options.addOption("h",false,"get usage");
+
+ options.addOption("s", true, "sequence database");
+- options.addOption("sge", false, "use SGE");
+ options.addOption("local", false, "use local system");
+ options.addOption("dna", false, "analyse dna, is default");
+ options.addOption("rna", false, "analyse rna");
+@@ -290,7 +289,6 @@
+ usageOptions.addOption("s", true, "sequence database");
+ usageOptions.addOption("g", true, "grammar file to analyse");
+ usageOptions.addOption("m", true, "model file to analyse");
+- usageOptions.addOption("sge", false, "use SGE");
+ usageOptions.addOption("local", false, "use local system");
+ usageOptions.addOption("dna", false, "analyse dna, is default");
+ usageOptions.addOption("rna", false, "analyse rna");
+@@ -355,11 +353,6 @@
+ type=LOCAL;
+ jobmngr = (JobManager) new LocalJobManager();
+ }
+- if( cmd.hasOption( "sge" ) ) {
+- logger.info("Using sge system");
+- type=SGE;
+- jobmngr = (JobManager) new SGEJobManager();
+- }
+ if( cmd.hasOption( "dna" ) ) {
+ format=1;
+ }
+--- a/src/org/irisa/genouest/logol/dispatcher/SGEJobManager.java
++++ b/src/org/irisa/genouest/logol/dispatcher/SGEJobManager.java
+@@ -5,10 +5,6 @@
+ import java.util.Vector;
+
+ import org.apache.log4j.Logger;
+-import org.ggf.drmaa.DrmaaException;
+-import org.ggf.drmaa.JobTemplate;
+-import org.ggf.drmaa.Session;
+-import org.ggf.drmaa.SessionFactory;
+ import org.irisa.genouest.logol.Constants;
+
+ /*
+@@ -18,111 +14,30 @@
+
+ private static final Logger logger = Logger.getLogger(org.irisa.genouest.logol.dispatcher.SGEJobManager.class);
+
+- private static String OS = System.getProperty("os.name").toLowerCase();
+-
+-
+- Vector<String> jobs = new Vector<String>();
+- Vector<String> jobsOutput = new Vector<String>();
+- Vector<String> jobsArgs = new Vector<String>();
+- Vector<String> jobIds = new Vector<String>();
+-
+- String arguments = "";
+-
+- static SessionFactory factory = null;
+- static Session session=null;
+-
+-
+- String jobId = null;
+-
+- String installPath=null;
+-
+ UUID uID = null;
+
+ public SGEJobManager() {
+- logger.info("Init DRM communication");
+- if(factory==null) {
+- factory = SessionFactory.getFactory();
+- }
+- if(session==null) {
+- session = factory.getSession();
+- }
+- if(session==null) {
+- logger.error(" Drm session could not open");
+- }
+- logger.info("DRM system: "+session.getDrmSystem());
+- try {
+- session.init("");
+- } catch (DrmaaException e) {
+- logger.error("Could not init the DRM session: "+e.getMessage());
+- }
++ logger.error("DRMAA not supported, libdrmaa-java not available in Debian");
+ }
+
+ public int addJob(String sequence, String output,String jobArgs) {
+- jobs.add(sequence);
+- jobsArgs.add(jobArgs);
+- jobsOutput.add(output);
+ return 0;
+ }
+
+ public int runJobs(String nativeSpecifications) {
+- JobTemplate jt;
+- for(int i=0;i<jobs.size();i++) {
+- try {
+- jt = session.createJobTemplate();
+- if(nativeSpecifications!=null) {
+- jt.setNativeSpecification(nativeSpecifications);
+- }
+-
+- jt.setJobName("LogolMatch");
+-
+- String out = jobsOutput.get(i);
+- // Redirect DRM streams
+- 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.setRemoteCommand("ruby");
+- }
+- else {
+- 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);
+- jobIds.add(jobId);
+- session.deleteJobTemplate(jt);
+- } catch (DrmaaException e) {
+- logger.error("Error during job submission: "+e.getMessage());
+- return -1;
+- }
+- }
+-
+-
++ logger.error("DRMAA not supported, libdrmaa-java not available in Debian");
+ return 0;
+ }
+
+ public int waitForJobsOver() {
+-
+- try {
+- session.synchronize(jobIds, Session.TIMEOUT_WAIT_FOREVER, true);
+- session.exit();
+- } catch (DrmaaException e) {
+- logger.error("Error during job submission: "+e.getMessage());
+- }
+- logger.info("Each sequence in bank resulted in a specific result file.");
+- for(int i=0;i<jobs.size();i++) {
+- logger.debug("Result file is available in work directory : "+jobsOutput.get(i));
+- }
++ logger.error("DRMAA not supported, libdrmaa-java not available in Debian");
+ return 0;
+ }
+
+ public void setJobArgs(String args) {
+- arguments=args;
+ }
+
+ public void setInstallPath(String installDir) {
+- installPath = installDir;
+-
+ }
+
+ }
Deleted: trunk/packages/logol/tags/1.7.2-1/debian/patches/series
===================================================================
--- trunk/packages/logol/trunk/debian/patches/series 2015-01-31 23:32:16 UTC (rev 18701)
+++ trunk/packages/logol/tags/1.7.2-1/debian/patches/series 2015-04-08 15:19:40 UTC (rev 19034)
@@ -1,5 +0,0 @@
-fixLibPath
-fixDrmmato6.2
-setDebianDirs
-fix_doc_generation
-remove_rubygems_usage
Copied: trunk/packages/logol/tags/1.7.2-1/debian/patches/series (from rev 18738, trunk/packages/logol/trunk/debian/patches/series)
===================================================================
--- trunk/packages/logol/tags/1.7.2-1/debian/patches/series (rev 0)
+++ trunk/packages/logol/tags/1.7.2-1/debian/patches/series 2015-04-08 15:19:40 UTC (rev 19034)
@@ -0,0 +1,6 @@
+remove_drmaa_support
+fixLibPath
+#fixDrmmato6.2
+setDebianDirs
+fix_doc_generation
+remove_rubygems_usage
Deleted: trunk/packages/logol/tags/1.7.2-1/debian/patches/setDebianDirs
===================================================================
--- trunk/packages/logol/trunk/debian/patches/setDebianDirs 2015-01-31 23:32:16 UTC (rev 18701)
+++ trunk/packages/logol/tags/1.7.2-1/debian/patches/setDebianDirs 2015-04-08 15:19:40 UTC (rev 19034)
@@ -1,55 +0,0 @@
-Subject: Use debian dirs for logs
-Description: Debian policy hierarchy use
-Author: Olivier Sallou <osallou at debian.org>
-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 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 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 $*
-
Copied: trunk/packages/logol/tags/1.7.2-1/debian/patches/setDebianDirs (from rev 19032, trunk/packages/logol/trunk/debian/patches/setDebianDirs)
===================================================================
--- trunk/packages/logol/tags/1.7.2-1/debian/patches/setDebianDirs (rev 0)
+++ trunk/packages/logol/tags/1.7.2-1/debian/patches/setDebianDirs 2015-04-08 15:19:40 UTC (rev 19034)
@@ -0,0 +1,55 @@
+Subject: Use debian dirs for logs
+Description: Debian policy hierarchy use
+Author: Olivier Sallou <osallou at debian.org>
+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 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 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
+@@ -25,5 +25,5 @@
+ JAVA_OPTS=" -Xms512m -Xmx4096m"
+ 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-1.4.2.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 $*
+
+--- a/LogolMultiExec.sh
++++ b/LogolMultiExec.sh
+@@ -28,5 +28,5 @@
+
+ echo "calling logol with parameters "$*
+
+-java $JAVA_OPTS -Dlogol.install=$LOGOL_HOME -Dlogol.conf=$LOGOL_HOME/prolog/logol.properties -Dlog4j.configuration=file://$LOGOL_LOG4J -classpath $LOGOL_HOME/lib/xalan.jar:$LOGOL_HOME/lib/xercesImpl.jar:$LOGOL_HOME/lib/xml-apis.jar:$LOGOL_HOME/lib/mail.jar:$LOGOL_HOME/lib/activation.jar:$LOGOL_HOME/lib/biojava.jar:$LOGOL_HOME/lib/bytecode:$LOGOL_HOME/lib/drmaa.jar:$LOGOL_HOME/lib/commons-configuration-1.5.jar:$LOGOL_HOME/lib/LogolExec.jar:$LOGOL_HOME/lib/commons-cli-1.1.jar:$LOGOL_HOME/lib/commons-collections-3.2.1.jar:$LOGOL_HOME/lib/commons-lang-2.4.jar:$LOGOL_HOME/lib/commons-logging-1.1.1.jar:$LOGOL_HOME/lib/log4j-1.2.15.jar:$LOGOL_HOME/lib/antlrworks-1.4.2.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 $*
+
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