Author: moeller Date: 2010-06-05 15:08:01 +0000 (Sat, 05 Jun 2010) New Revision: 4875
Added: trunk/packages/gentle/trunk/debian/GENtle.1 trunk/packages/gentle/trunk/debian/patches/remove_clustalw.patch Removed: trunk/packages/gentle/trunk/debian/gentle.1 Modified: trunk/packages/gentle/trunk/debian/changelog trunk/packages/gentle/trunk/debian/control trunk/packages/gentle/trunk/debian/copyright trunk/packages/gentle/trunk/debian/docs trunk/packages/gentle/trunk/debian/files trunk/packages/gentle/trunk/debian/gentle.install trunk/packages/gentle/trunk/debian/manpages trunk/packages/gentle/trunk/debian/patches/series trunk/packages/gentle/trunk/debian/rules Log: Further adjustments to remove clustalw, prepare -dbg package (which does not work) and lintian cleanliness. Copied: trunk/packages/gentle/trunk/debian/GENtle.1 (from rev 4857, trunk/packages/gentle/trunk/debian/gentle.1) =================================================================== --- trunk/packages/gentle/trunk/debian/GENtle.1 (rev 0) +++ trunk/packages/gentle/trunk/debian/GENtle.1 2010-06-05 15:08:01 UTC (rev 4875) @@ -0,0 +1,22 @@ +.\" 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 <[email protected]>, +for the Debian project (and may be used by others). Modified: trunk/packages/gentle/trunk/debian/changelog =================================================================== --- trunk/packages/gentle/trunk/debian/changelog 2010-06-05 12:39:30 UTC (rev 4874) +++ trunk/packages/gentle/trunk/debian/changelog 2010-06-05 15:08:01 UTC (rev 4875) @@ -1,13 +1,19 @@ -gentle (1.9+cvs20100602+dfsg-1) experimental; urgency=low +gentle (1.9+cvs20100602+dfsg-1) unstable; urgency=low * Reupload in reaction to ftp-masters comments (Closes: #582959) - * removed tinyurl + * 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 * added gentle-dbg package + * compilation successfullly tested against gcc-4.5 + * added help/* to package + * reupload to unstable -- Steffen Moeller <[email protected]> Wed, 02 Jun 2010 12:07:21 +0200 Modified: trunk/packages/gentle/trunk/debian/control =================================================================== --- trunk/packages/gentle/trunk/debian/control 2010-06-05 12:39:30 UTC (rev 4874) +++ trunk/packages/gentle/trunk/debian/control 2010-06-05 15:08:01 UTC (rev 4875) @@ -1,8 +1,8 @@ Source: gentle -Section: non-free/science +Section: science Priority: optional Maintainer: Steffen Moeller <[email protected]> -Build-Depends: debhelper (>= 7), autotools-dev, libwxgtk2.8-dev, quilt, cdbs, libtinyxml-dev +Build-Depends: debhelper (>= 7), autotools-dev, libwxgtk2.8-dev, quilt, cdbs, libtinyxml-dev, automake, autoconf Standards-Version: 3.8.4 Homepage: http://gentle.magnusmanske.de Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/gentle/trunk/?rev=0&sc=0 @@ -11,6 +11,7 @@ Package: gentle Architecture: any Depends: ${shlibs:Depends}, ${misc:Depends} +Recommends: clustalw 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 @@ -19,10 +20,15 @@ Package: gentle-dbg Architecture: any Depends: gentle, ${shlibs:Depends}, ${misc:Depends} +Section: debug +Priority: extra Recommends: 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. + . + Well, this package is not functional for the time speaking. + Help would be appreciated. Modified: trunk/packages/gentle/trunk/debian/copyright =================================================================== --- trunk/packages/gentle/trunk/debian/copyright 2010-06-05 12:39:30 UTC (rev 4874) +++ trunk/packages/gentle/trunk/debian/copyright 2010-06-05 15:08:01 UTC (rev 4875) @@ -6,45 +6,15 @@ http://gentle.magnusmanske.de/ -Files: clustalw/* +Files: ipc/* +Author: Dirk Nolting <[email protected]> +Copyright: (C) 2001 Dirk Nolting <[email protected]> +License: GPL-2+ -Upstream Authors: - Toby J. Gibson <[email protected]> - J. D. Thompson <[email protected]> - Des G. Higgins <[email protected]> +Files: wav/* +Copyright: Voxeo Corporation (http://evolution.voxeo.com) +License: LGPL -Copyright: - The authors and their respective employers. - -License: - - ****************************************************************************** - - CLUSTAL W Multiple Sequence Alignment Program - (version 1.83, Feb 2003) - - ****************************************************************************** - - - Please send bug reports, comments etc. to one of:- - [email protected] - [email protected] - [email protected] - - - ****************************************************************************** - - POLICY ON COMMERCIAL DISTRIBUTION OF CLUSTAL W - - Clustal W is freely available to the user community. However, Clustal W is - increasingly being distributed as part of commercial sequence analysis - packages. To help us safeguard future maintenance and development, commercial - distributors of Clustal W must take out a NON-EXCLUSIVE LICENCE. Anyone - wishing to commercially distribute version 1.81 of Clustal W should contact the - authors unless they have previously taken out a licence. - - ****************************************************************************** - Files: * Upstream Author: Modified: trunk/packages/gentle/trunk/debian/docs =================================================================== --- trunk/packages/gentle/trunk/debian/docs 2010-06-05 12:39:30 UTC (rev 4874) +++ trunk/packages/gentle/trunk/debian/docs 2010-06-05 15:08:01 UTC (rev 4875) @@ -1,5 +1,4 @@ docs/GENtle*en*.pdf NEWS -README.Ubuntu RELEASE-NOTES.txt tips_en.txt Modified: trunk/packages/gentle/trunk/debian/files =================================================================== --- trunk/packages/gentle/trunk/debian/files 2010-06-05 12:39:30 UTC (rev 4874) +++ trunk/packages/gentle/trunk/debian/files 2010-06-05 15:08:01 UTC (rev 4875) @@ -1 +1,4 @@ -gentle_1.9+cvs20100308-1_amd64.deb non-free/science optional +gentle_1.9+cvs20100602+dfsg-1_amd64.deb science optional +gentle-dbg_1.9+cvs20100602+dfsg-1_amd64.deb debug extra +gentle_1.9+cvs20100602+dfsg-1_amd64.deb science optional +gentle-dbg_1.9+cvs20100602+dfsg-1_amd64.deb debug extra Deleted: trunk/packages/gentle/trunk/debian/gentle.1 =================================================================== --- trunk/packages/gentle/trunk/debian/gentle.1 2010-06-05 12:39:30 UTC (rev 4874) +++ trunk/packages/gentle/trunk/debian/gentle.1 2010-06-05 15:08:01 UTC (rev 4875) @@ -1,22 +0,0 @@ -.\" 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 <[email protected]>, -for the Debian project (and may be used by others). Modified: trunk/packages/gentle/trunk/debian/gentle.install =================================================================== --- trunk/packages/gentle/trunk/debian/gentle.install 2010-06-05 12:39:30 UTC (rev 4874) +++ trunk/packages/gentle/trunk/debian/gentle.install 2010-06-05 15:08:01 UTC (rev 4875) @@ -1,4 +1,5 @@ wav /usr/share/gentle/ +help /usr/share/gentle/ variables.csv /usr/share/gentle/ bitmaps /usr/share/gentle/ codon_catalog.csv /usr/share/gentle/ Modified: trunk/packages/gentle/trunk/debian/manpages =================================================================== --- trunk/packages/gentle/trunk/debian/manpages 2010-06-05 12:39:30 UTC (rev 4874) +++ trunk/packages/gentle/trunk/debian/manpages 2010-06-05 15:08:01 UTC (rev 4875) @@ -1 +1 @@ -debian/gentle.1 +debian/GENtle.1 Added: trunk/packages/gentle/trunk/debian/patches/remove_clustalw.patch =================================================================== --- trunk/packages/gentle/trunk/debian/patches/remove_clustalw.patch (rev 0) +++ trunk/packages/gentle/trunk/debian/patches/remove_clustalw.patch 2010-06-05 15:08:01 UTC (rev 4875) @@ -0,0 +1,42 @@ +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\ Modified: trunk/packages/gentle/trunk/debian/patches/series =================================================================== --- trunk/packages/gentle/trunk/debian/patches/series 2010-06-05 12:39:30 UTC (rev 4874) +++ trunk/packages/gentle/trunk/debian/patches/series 2010-06-05 15:08:01 UTC (rev 4875) @@ -1 +1,2 @@ remove_tinyxml.patch +remove_clustalw.patch Modified: trunk/packages/gentle/trunk/debian/rules =================================================================== --- trunk/packages/gentle/trunk/debian/rules 2010-06-05 12:39:30 UTC (rev 4874) +++ trunk/packages/gentle/trunk/debian/rules 2010-06-05 15:08:01 UTC (rev 4875) @@ -11,9 +11,9 @@ include /usr/share/cdbs/1/rules/patchsys-quilt.mk -CXXFLAGS="-D__DEBIAN__ -O2 -g -Wno-write-strings" +CXXFLAGS="-D__DEBIAN__ -O2 -g -Wno-write-strings -DUSE_EXTERNAL_CLUSTALW" -configure: patch configure-stamp +configure: configure-stamp configure-stamp: dh_testdir echo "configuring with own configure!" @@ -24,7 +24,7 @@ touch $@ build build-arch: build-stamp -build-stamp: configure-stamp +build-stamp: patch configure-stamp dh_testdir echo "building with own build!" $(MAKE) CXXFLAGS=$(CXXFLAGS) @@ -52,6 +52,9 @@ dh_builddeb install install-arch: build-stamp + dh_install + find debian -name "*.png" -o -name "*.htm" -o -name "*.xpm" -o -name "*.bmp" -o "*.txt" -o "*.csv" | xargs -r chmod -x + find debian -name "license.txt" | xargs -r rm install-indep: echo Nothing to do for install-indep @@ -60,7 +63,7 @@ #$(MAKE) -f debian/rules DH_OPTIONS=-i binary-common echo Nothing to do for binary-indep -binary-arch: build-arch +binary-arch: install-arch $(MAKE) -f debian/rules DH_OPTIONS=-s binary-common binary: binary-arch binary-indep @@ -69,7 +72,7 @@ dh_testdir dh_testroot find . -name "*.o" | xargs -r rm - dh_clean build-arch-stamp build-indep-stamp configure-stamp + dh_clean build-arch-stamp build-indep-stamp configure-stamp build-stamp @@ -87,5 +90,6 @@ cvs -z3 -d:pserver:[email protected]:/cvsroot/gentle-m co -P GENtle mv GENtle "gentle-$(VERSION)" GZIP=-9 tar --exclude Makefile.in --exclude Makefile --exclude CVS --exclude tinyxml \ - --exclude .deps --exclude .cvsignore \ + --exclude .deps --exclude .cvsignore --exclude Makefile.in --exclude Makefile.linux \ + --exclude clustalw \ -czvf "gentle_$(VERSION).orig.tar.gz" "gentle-$(VERSION)" _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
