debian/0000775000000000000000000000000012121111651007157 5ustar debian/gentle.dirs0000664000000000000000000000005311377055423011336 0ustar /usr /usr/bin /usr/share /usr/share/gentle debian/control0000664000000000000000000000270712121111520010563 0ustar Source: gentle Section: science Priority: optional Maintainer: Ubuntu Developers XSBC-Original-Maintainer: Debian Med Packaging Team Uploaders: Steffen Moeller , Andreas Tille Build-Depends: debhelper (>= 7), libwxgtk2.8-dev, libtinyxml-dev, dh-autoreconf, libmysqlclient-dev, libsqlite3-dev Standards-Version: 3.9.4 Homepage: http://gentle.magnusmanske.de Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gentle/trunk/ Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/gentle/trunk/ Package: gentle Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} Recommends: clustalw (>= 2.1+lgpl) Description: suite to plan genetic cloning GENtle is a software for DNA and amino acid editing, database management, plasmid maps, restriction and ligation, alignments, sequencer data import, calculators, gel image display, PCR, and much more. #Package: gentle-dbg #Architecture: any #Depends: gentle, ${shlibs:Depends}, ${misc:Depends} #Priority: extra #Recommends: libtinyxml2.6.2-dbg|libtinyxml2.5.3-dbg #Description: debug symbols for gentle suite for genetic cloning # As every suite working with a series of independently developed # programs, also GENtle tends to be perceived as rather complex. # This package prepares users and developers to communicate # over hunting and eliminating bugs. # # Why doesn't this work? debian/GENtle.10000664000000000000000000000124711402464121010367 0ustar .\" Hey, EMACS: -*- nroff -*- .TH GENTLE 1 "March 9, 2010" .SH NAME GENtle \- program to plan genetic cloning experiments .SH SYNOPSIS .B gentle .SH DESCRIPTION GENtle integrates a series of programs and databases to plan the integration of foreign DNA into another larger DNA that by some means can replicate itself or is by some other means replicated - a process commonly referred to as .I cloning. .SH OPTIONS None. .SH SEE ALSO .BR http://gentle.magnusmanske.de .SH AUTHOR GENtle was written by Magnus Manske. .PP This manual page was written by Steffen Moeller , for the Debian project (and may be used by others). debian/manpages0000664000000000000000000000002011402464121010671 0ustar debian/GENtle.1 debian/README.source0000664000000000000000000000072511403267463011361 0ustar GENtle for Debian ----------------- The sources were taken from the CVS repository, removed are - the CVS directories - the tinyxml directory (since redundant with Debian's libtinyxml) - the clustalw directory (since redundant and non-free) - ncoils.cpp,ncoils.h and the coils directory Patches: remove_tinyxml.patch - small changes to Makefile.am since tinyurl is now gone remove_clustalw.patch - small changes to Makefile.am since clustalw is now gone debian/copyright0000664000000000000000000000237212037243744011135 0ustar This work was packaged for Debian by: Steffen Moeller on Tue, 09 Mar 2010 10:42:41 +0100 It was downloaded from: http://gentle.magnusmanske.de/ Files: ipc/* Author: Dirk Nolting Copyright: (C) 2001 Dirk Nolting License: GPL-2+ Files: wav/* Copyright: Voxeo Corporation (http://evolution.voxeo.com) License: LGPL-3 Files: ncoils.h ncoild.cpp coils/* Authors: Rob Russel Larry Harvie Reinhard Schneider Copyright: EMBL Heidelberg License: GPL-2+ Source: Adapted from http://www.russell.embl.de/cgi-bin/coils-svr.pl Files: * Upstream Author: Magnus Manske Copyright: Magnus Manske License: GPL-3+ On Debian systems, the complete text of the GNU General Public License version 3 can be found in "/usr/share/common-licenses/GPL-3", version 2 can be found in "/usr/share/common-licenses/GPL-2". The LGPL is found in "/usr/share/common-licenses/LGPL-3". The Debian packaging is: Copyright (C) 2010 Steffen Moeller and is licensed under the GPL version 3, see above. debian/docs0000664000000000000000000000006711402464121010041 0ustar docs/GENtle*en*.pdf NEWS RELEASE-NOTES.txt tips_en.txt debian/patches/0000775000000000000000000000000012121111651010606 5ustar debian/patches/remove_clustalw.patch0000664000000000000000000000204611402464121015050 0ustar Index: gentle-1.9+20100602+dfsg/Makefile.am =================================================================== --- gentle-1.9+20100602+dfsg.orig/Makefile.am 2010-06-05 16:36:41.000000000 +0200 +++ gentle-1.9+20100602+dfsg/Makefile.am 2010-06-05 16:36:41.000000000 +0200 @@ -137,24 +137,6 @@ TPhyloTree.cpp\ PCR_Troubleshoot.cpp\ TProteolysis.cpp\ -clustalw/alnscore.cpp\ -clustalw/amenu.cpp\ -clustalw/calcgap.cpp\ -clustalw/calcprf1.cpp\ -clustalw/calcprf2.cpp\ -clustalw/calctree.cpp\ -clustalw/clustalw.cpp\ -clustalw/gcgcheck.cpp\ -clustalw/interfac.cpp\ -clustalw/malign.cpp\ -clustalw/palign.cpp\ -clustalw/prfalign.cpp\ -clustalw/random.cpp\ -clustalw/readmat.cpp\ -clustalw/sequence.cpp\ -clustalw/showpair.cpp\ -clustalw/trees.cpp\ -clustalw/util.cpp\ ipc/element.cpp\ ipc/gp_out.cpp\ ipc/ipc.cpp\ @@ -231,12 +213,6 @@ TPhyloTree.h\ TEliteLaChromLogDialog.h\ ncoils.h\ -clustalw/clustalw.h\ -clustalw/dayhoff.h \ -clustalw/general.h \ -clustalw/matrices.h \ -clustalw/param.h \ -clustalw/xmenu.h\ ipc/element.h\ ipc/global.h\ ipc/gp_out.h\ debian/patches/remove_tinyxml.patch0000664000000000000000000000524111401537261014723 0ustar Index: gentle-1.9+20100602+dfsg/Makefile.am =================================================================== --- gentle-1.9+20100602+dfsg.orig/Makefile.am 2010-06-02 11:08:25.000000000 +0200 +++ gentle-1.9+20100602+dfsg/Makefile.am 2010-06-02 11:10:15.000000000 +0200 @@ -63,7 +63,7 @@ bitmaps/scissors.bmp -GENtle_LDADD = $(WX_LIBS) -L/usr/lib -L/usr/local/lib -lsqlite -lsqlite3 -lmysqlclient +GENtle_LDADD = $(WX_LIBS) -L/usr/lib -L/usr/local/lib -lsqlite -lsqlite3 -lmysqlclient -ltinyxml GENtle_LDFLAGS = -s GENtle_SOURCES = TXMLfile.cpp\ TVectorTree.cpp\ @@ -137,10 +137,6 @@ TPhyloTree.cpp\ PCR_Troubleshoot.cpp\ TProteolysis.cpp\ -tinyxml/tinyxmlparser.cpp\ -tinyxml/tinyxmlerror.cpp\ -tinyxml/tinyxml.cpp\ -tinyxml/tinystr.cpp\ clustalw/alnscore.cpp\ clustalw/amenu.cpp\ clustalw/calcgap.cpp\ @@ -235,8 +231,6 @@ TPhyloTree.h\ TEliteLaChromLogDialog.h\ ncoils.h\ -tinyxml/tinyxml.h\ -tinyxml/tinystr.h\ clustalw/clustalw.h\ clustalw/dayhoff.h \ clustalw/general.h \ Index: gentle-1.9+20100602+dfsg/main.h =================================================================== --- gentle-1.9+20100602+dfsg.orig/main.h 2010-06-02 22:02:39.000000000 +0200 +++ gentle-1.9+20100602+dfsg/main.h 2010-06-02 22:03:57.000000000 +0200 @@ -129,7 +129,11 @@ // Don't you *EVER* turn this on again!!!! //#define TIXML_USE_STL +#ifndef __DEBIAN__ #include "tinyxml/tinyxml.h" +#else +#include "tinyxml.h" +#endif #include #include Index: gentle-1.9+20100602+dfsg/TXMLfile.cpp =================================================================== --- gentle-1.9+20100602+dfsg.orig/TXMLfile.cpp 2010-06-02 22:07:18.000000000 +0200 +++ gentle-1.9+20100602+dfsg/TXMLfile.cpp 2010-06-02 22:22:56.000000000 +0200 @@ -50,7 +50,7 @@ analyze ( doc ) ; } -void TXMLfile::analyze ( const TiXmlDocument &doc ) +void TXMLfile::analyze ( TiXmlDocument &doc ) { if ( doc.FirstChild ( "GBSeq" ) ) { Index: gentle-1.9+20100602+dfsg/TXMLfile.h =================================================================== --- gentle-1.9+20100602+dfsg.orig/TXMLfile.h 2010-06-02 22:13:31.000000000 +0200 +++ gentle-1.9+20100602+dfsg/TXMLfile.h 2010-06-02 22:22:32.000000000 +0200 @@ -25,7 +25,7 @@ TVector *getVector ( int a ) ; ///< Returns pointer to one of the vectors private : - void analyze ( const TiXmlDocument &doc ) ; ///< Parse single/multiple sequences + void analyze ( TiXmlDocument &doc ) ; ///< Parse single/multiple sequences void readGBSeq ( TiXmlNode *base ) ; ///< The actual parser wxString t ( TiXmlText *txt ) ; ///< Safe text conversion wxString t ( const char *txt ) ; ///< Safe text conversion debian/patches/forward_slashes.patch0000664000000000000000000000116111415434145015027 0ustar Index: gentle-1.9+cvs20100605+dfsg/MyFrame.cpp =================================================================== --- gentle-1.9+cvs20100605+dfsg.orig/MyFrame.cpp 2010-06-17 18:31:13.000000000 +0200 +++ gentle-1.9+cvs20100605+dfsg/MyFrame.cpp 2010-06-17 18:33:38.000000000 +0200 @@ -586,7 +586,7 @@ { wxHtmlHelpController *hc = new wxHtmlHelpController ( wxHF_DEFAULT_STYLE|wxHF_OPEN_FILES ) ; helpfile += myapp()->homedir ; - helpfile += _T("\\help\\") ; + helpfile += _T("/help/") ; helpfile += lang_string ; helpfile += _T(".hhp") ; hc->AddBook ( helpfile ) ; debian/patches/series0000664000000000000000000000013112121111624012016 0ustar forward_slashes.patch remove_tinyxml.patch remove_clustalw.patch remove-sqlite-dep.patch debian/patches/remove-sqlite-dep.patch0000664000000000000000000000077512121111646015206 0ustar Description: remove unused sqlite dep Author: Dmitrijs Ledkovs --- gentle-1.9+cvs20100605+dfsg1.orig/Makefile.am +++ gentle-1.9+cvs20100605+dfsg1/Makefile.am @@ -63,7 +63,7 @@ bitmaps/print.bmp \ bitmaps/scissors.bmp -GENtle_LDADD = $(WX_LIBS) -L/usr/lib -L/usr/local/lib -lsqlite -lsqlite3 -lmysqlclient -ltinyxml +GENtle_LDADD = $(WX_LIBS) -L/usr/lib -L/usr/local/lib -lsqlite3 -lmysqlclient -ltinyxml GENtle_LDFLAGS = -s GENtle_SOURCES = TXMLfile.cpp\ TVectorTree.cpp\ debian/compat0000664000000000000000000000000211377055423010375 0ustar 7 debian/rules0000775000000000000000000000520512121111576010247 0ustar #!/usr/bin/make -f # -*- makefile -*- # Sample debian/rules that uses debhelper. # This file was originally written by Joey Hess and Craig Small. # As a special exception, when this file is copied by dh-make into a # dh-make output file, you may use that output file without restriction. # This special exception was added by Craig Small in version 0.37 of dh-make. # Uncomment this to turn on verbose mode. export DH_VERBOSE=1 CXXFLAGS="-D__DEBIAN__ -O2 -g -Wno-write-strings -DUSE_EXTERNAL_CLUSTALW" configure: configure-stamp configure-stamp: dh_testdir echo "configuring with own configure!" dh_autoreconf CXXFLAGS=$(CXXFLAGS) ./configure --prefix=/usr for i in help/*.html help/*.css *.db help/*.htm */*.png */*.x[bp]m */*.bmp *.txt */*.txt *.csv; do chmod -x "$$i"; done touch $@ build build-arch: build-stamp build-stamp: configure-stamp dh_testdir echo "building with own build!" $(MAKE) CXXFLAGS=$(CXXFLAGS) touch $@ build-indep: echo "Nothing to do for build-indep" binary-common: dh_testdir dh_testroot dh_installchangelogs dh_installdocs dh_installexamples dh_installman dh_link #dh_strip --dbg-package=gentle-dbg dh_strip dh_compress -X.pdf dh_fixperms dh_makeshlibs dh_installdeb dh_shlibdeps dh_gencontrol dh_md5sums dh_builddeb install install-arch: build-stamp dh_install find debian -name "license.txt" | xargs -r rm install-indep: echo Nothing to do for install-indep binary-indep: #$(MAKE) -f debian/rules DH_OPTIONS=-i binary-common echo Nothing to do for binary-indep binary-arch: install-arch $(MAKE) -f debian/rules DH_OPTIONS=-s binary-common binary: binary-arch binary-indep clean:: dh_testdir dh_testroot find . -name "*.o" | xargs -r rm rm -f GENtle dh_autoreconf_clean dh_clean build-arch-stamp build-indep-stamp configure-stamp build-stamp COMPRESSION=xz VERSION=1.9+cvs$(shell date +"%Y%m%d"|tr -d ' \t\n')~dfsg get-orig-source: dh_testdir if [ -d GENtle ]; then \ echo "Previous checkout exists as folder 'GENtle', please remove." ; \ exit -1 ; \ fi if [ -d "gentle-$(VERSION)" ]; then \ echo "Previous checkout exists as folder 'gentle-$(VERSION)', please remove." ; \ exit -1 ; \ fi cvs -z3 -d:pserver:anonymous@gentle-m.cvs.sourceforge.net:/cvsroot/gentle-m co -P GENtle mv GENtle "gentle-$(VERSION)" find . -name "*.dll" -delete find . -name "*.a" -delete GZIP="--best --no-name" tar --exclude Makefile.in --exclude Makefile --exclude CVS --exclude tinyxml \ --exclude .deps --exclude .cvsignore --exclude Makefile.in --exclude Makefile.linux \ --exclude clustalw \ -caf "../gentle_$(VERSION).orig.tar.$(COMPRESSION)" "gentle-$(VERSION)" rm "gentle-$(VERSION)" debian/gentle.doc-base0000664000000000000000000000037611401544762012057 0ustar Document: gentle Title: Gentle Manual Author: Magnus Manske Abstract: The manual presents an overview on the functionalities that GENtle contributes to the cloning process. Section: Science/Biology Format: pdf Files: /usr/share/doc/gentle/GENtle*.pdf debian/menu0000664000000000000000000000015011377055423010062 0ustar ?package(gentle):needs="X11" section="Applications/Science"\ title="GENtle" command="/usr/bin/GENtle" debian/README.Debian0000664000000000000000000000112511403267463011236 0ustar gentle for Debian ----------------- GENtle ships a programs that Debian has in the past indicates as non-free, i.e. ClustalW. It is redundant with the clustalw program that is already in the archive, and so is the tinyxml library. Both folders have been removed from the source tree for this upload to achieve DFSG compliance. The coils package is available under the GPL, so it does not need to be separated for licensing issues. A later upload should however consider the distribution of coils as a separate package. -- Steffen Moeller Tue, 08 Jun 2010 00:12:15 +0200 debian/upstream0000664000000000000000000000037511756674216010777 0ustar Reference: Author: Magnus Manske Title: "GENtle, a free multi-purpose molecular biology tool" Year: 2006 URL: http://www.scientificcommons.org/20178091 eprint: http://kups.ub.uni-koeln.de/1907/1/GENtle.pdf publisher: "Universität zu Köln" debian/changelog0000664000000000000000000000453312121111454011037 0ustar gentle (1.9+cvs20100605+dfsg1-1ubuntu1) raring; urgency=low * Drop sqlite0-dev build-dep. * Do not pointlessly link with sqlite. -- Dmitrijs Ledkovs Sat, 16 Mar 2013 14:37:00 +0000 gentle (1.9+cvs20100605+dfsg1-1) unstable; urgency=low * debian/rules: - Make sure that binary dlls will be deleted when unpacking Closes: #685149 - Use xz compression for upstream source - Drop *.a files from upstream source in get-orig-source target * Versioned depends from DFSG free clustalw -> package can go to main * debian/control: - fix broken VCS fields - Standards-Version: 3.9.4 (no changes needed) * debian/upstream: Add citation information -- Andreas Tille Fri, 17 Aug 2012 14:36:52 +0200 gentle (1.9+cvs20100605+dfsg-3) unstable; urgency=low * Updated policy to 3.9.2 * Rebuilt against later versions of mysql and tinyxml libraries -- Steffen Moeller Fri, 03 Jun 2011 21:12:05 +0200 gentle (1.9+cvs20100605+dfsg-2) unstable; urgency=low * Adding build-dependency to libmysqlclient-dev (Closes: #585891) and to libsqlite3-dev, libsqlite0-dev * Changed format to 3.0 (quilt), removed dependency to cdbs and quilt, simplified debian/rules accordingly. * improved get-orig-source to remove directory checked out -- Steffen Moeller Tue, 15 Jun 2010 16:38:33 +0200 gentle (1.9+cvs20100605+dfsg-1) unstable; urgency=low * Reupload in reaction to ftp-masters comments (Closes: #582959) * removed tinyurl and clustalw from source tree for DFSG compatibility - which introduced dependency to quilt - and provoked +dfsg suffix to version (not fully correct, yet) * invoking automake, autoconf during build - added those to build-dependencies - removed upstream Makefile and Makefile.in from source * declared 1.0 source format * removed doc-base lintian warning * explicitly listing man page as such, now correctly named GENtle.1 * prepared for eventually adding gentle-dbg * compilation successfullly tested against gcc-4.5 * added help/* to package * reupload to unstable -- Steffen Moeller Wed, 02 Jun 2010 12:07:21 +0200 gentle (1.9+cvs20100531-1) experimental; urgency=low * Initial release. -- Steffen Moeller Tue, 25 May 2010 00:08:31 +0200 debian/source/0000775000000000000000000000000011572231045010470 5ustar debian/source/format0000664000000000000000000000001411405721605011677 0ustar 3.0 (quilt) debian/gentle.install0000664000000000000000000000047711402464121012041 0ustar wav /usr/share/gentle/ help /usr/share/gentle/ variables.csv /usr/share/gentle/ bitmaps /usr/share/gentle/ codon_catalog.csv /usr/share/gentle/ marker.txt /usr/share/gentle/ ncoils.matrix /usr/share/gentle/ default.tab /usr/share/gentle/ commonvectors.db /usr/share/gentle/ blank.db /usr/share/gentle/ GENtle /usr/bin/