Author: moeller Date: 2010-05-25 23:19:47 +0000 (Tue, 25 May 2010) New Revision: 4839
Added: trunk/packages/gentle/ trunk/packages/gentle/trunk/ trunk/packages/gentle/trunk/debian/ trunk/packages/gentle/trunk/debian/README.Debian trunk/packages/gentle/trunk/debian/README.source trunk/packages/gentle/trunk/debian/changelog trunk/packages/gentle/trunk/debian/compat 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.dirs trunk/packages/gentle/trunk/debian/gentle.doc-base trunk/packages/gentle/trunk/debian/gentle.install trunk/packages/gentle/trunk/debian/manpage.1 trunk/packages/gentle/trunk/debian/menu trunk/packages/gentle/trunk/debian/rules Log: GENtle is a package for the molecular cloning of DNA/RNA. It is already in new, but not really DFSG compatible since it ships sources of clustalw. Well, it is a start and for experimental it should be fine. Property changes on: trunk/packages/gentle/trunk/debian ___________________________________________________________________ Added: mergeWithUpstream + 1 Added: trunk/packages/gentle/trunk/debian/README.Debian =================================================================== --- trunk/packages/gentle/trunk/debian/README.Debian (rev 0) +++ trunk/packages/gentle/trunk/debian/README.Debian 2010-05-25 23:19:47 UTC (rev 4839) @@ -0,0 +1,7 @@ +gentle for Debian +----------------- + +GENtle ships a series of sources of programs that Debian +has in the past indicates as non-free. + + -- Steffen Moeller <[email protected]> Tue, 09 Mar 2010 10:42:41 +0100 Added: trunk/packages/gentle/trunk/debian/README.source =================================================================== --- trunk/packages/gentle/trunk/debian/README.source (rev 0) +++ trunk/packages/gentle/trunk/debian/README.source 2010-05-25 23:19:47 UTC (rev 4839) @@ -0,0 +1,10 @@ +GENtle for Debian +----------------- + +The sources were taken from the CVS repository +with the CVS directories removed. + +A later upload will also have the clustalw +folder removed for full dfsg compliance. + + Added: trunk/packages/gentle/trunk/debian/changelog =================================================================== --- trunk/packages/gentle/trunk/debian/changelog (rev 0) +++ trunk/packages/gentle/trunk/debian/changelog 2010-05-25 23:19:47 UTC (rev 4839) @@ -0,0 +1,5 @@ +gentle (1.9+cvs20100531-1) experimental; urgency=low + + * Initial release (Closes: #582959) + + -- Steffen Moeller <[email protected]> Tue, 25 May 2010 00:08:31 +0200 Added: trunk/packages/gentle/trunk/debian/compat =================================================================== --- trunk/packages/gentle/trunk/debian/compat (rev 0) +++ trunk/packages/gentle/trunk/debian/compat 2010-05-25 23:19:47 UTC (rev 4839) @@ -0,0 +1 @@ +7 Added: trunk/packages/gentle/trunk/debian/control =================================================================== --- trunk/packages/gentle/trunk/debian/control (rev 0) +++ trunk/packages/gentle/trunk/debian/control 2010-05-25 23:19:47 UTC (rev 4839) @@ -0,0 +1,15 @@ +Source: gentle +Section: non-free/science +Priority: optional +Maintainer: Steffen Moeller <[email protected]> +Build-Depends: debhelper (>= 7), autotools-dev, libwxgtk2.8-dev +Standards-Version: 3.8.4 +Homepage: http://gentle.magnusmanske.de + +Package: gentle +Architecture: any +Depends: ${shlibs:Depends}, ${misc:Depends} +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. Added: trunk/packages/gentle/trunk/debian/copyright =================================================================== --- trunk/packages/gentle/trunk/debian/copyright (rev 0) +++ trunk/packages/gentle/trunk/debian/copyright 2010-05-25 23:19:47 UTC (rev 4839) @@ -0,0 +1,78 @@ +This work was packaged for Debian by: + + Steffen Moeller <[email protected]> on Tue, 09 Mar 2010 10:42:41 +0100 + +It was downloaded from: + + http://gentle.magnusmanske.de/ + +Files: clustalw/* + +Upstream Authors: + Toby J. Gibson <[email protected]> + J. D. Thompson <[email protected]> + Des G. Higgins <[email protected]> + +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: + Magnus Manske <[email protected]> + +Copyright: + Magnus Manske <[email protected]> + +License: + + This program 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 3 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 <http://www.gnu.org/licenses/>. + +On Debian systems, the complete text of the GNU General +Public License version 3 can be found in "/usr/share/common-licenses/GPL-3". + +The Debian packaging is: + + Copyright (C) 2010 Steffen Moeller <[email protected]> + +and is licensed under the GPL version 3, see above. Added: trunk/packages/gentle/trunk/debian/docs =================================================================== --- trunk/packages/gentle/trunk/debian/docs (rev 0) +++ trunk/packages/gentle/trunk/debian/docs 2010-05-25 23:19:47 UTC (rev 4839) @@ -0,0 +1,5 @@ +docs/GENtle*en*.pdf +NEWS +README.Ubuntu +RELEASE-NOTES.txt +tips_en.txt Added: trunk/packages/gentle/trunk/debian/files =================================================================== --- trunk/packages/gentle/trunk/debian/files (rev 0) +++ trunk/packages/gentle/trunk/debian/files 2010-05-25 23:19:47 UTC (rev 4839) @@ -0,0 +1 @@ +gentle_1.9+cvs20100308-1_amd64.deb non-free/science optional Added: trunk/packages/gentle/trunk/debian/gentle.dirs =================================================================== --- trunk/packages/gentle/trunk/debian/gentle.dirs (rev 0) +++ trunk/packages/gentle/trunk/debian/gentle.dirs 2010-05-25 23:19:47 UTC (rev 4839) @@ -0,0 +1,4 @@ +/usr +/usr/bin +/usr/share +/usr/share/gentle Added: trunk/packages/gentle/trunk/debian/gentle.doc-base =================================================================== --- trunk/packages/gentle/trunk/debian/gentle.doc-base (rev 0) +++ trunk/packages/gentle/trunk/debian/gentle.doc-base 2010-05-25 23:19:47 UTC (rev 4839) @@ -0,0 +1,10 @@ +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 + +Format: pdf +Files: /usr/share/doc/gentle/GENtle*.pdf Added: trunk/packages/gentle/trunk/debian/gentle.install =================================================================== --- trunk/packages/gentle/trunk/debian/gentle.install (rev 0) +++ trunk/packages/gentle/trunk/debian/gentle.install 2010-05-25 23:19:47 UTC (rev 4839) @@ -0,0 +1,9 @@ +wav /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/ Added: trunk/packages/gentle/trunk/debian/manpage.1 =================================================================== --- trunk/packages/gentle/trunk/debian/manpage.1 (rev 0) +++ trunk/packages/gentle/trunk/debian/manpage.1 2010-05-25 23:19:47 UTC (rev 4839) @@ -0,0 +1,22 @@ +.\" Hey, EMACS: -*- nroff -*- +.TH GENTLE SECTION "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). Added: trunk/packages/gentle/trunk/debian/menu =================================================================== --- trunk/packages/gentle/trunk/debian/menu (rev 0) +++ trunk/packages/gentle/trunk/debian/menu 2010-05-25 23:19:47 UTC (rev 4839) @@ -0,0 +1,2 @@ +?package(gentle):needs="X11" section="Applications/Science"\ + title="GENtle" command="/usr/bin/GENtle" Added: trunk/packages/gentle/trunk/debian/rules =================================================================== --- trunk/packages/gentle/trunk/debian/rules (rev 0) +++ trunk/packages/gentle/trunk/debian/rules 2010-05-25 23:19:47 UTC (rev 4839) @@ -0,0 +1,76 @@ +#!/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" + +configure: configure-stamp +configure-stamp: + dh_testdir + echo "configuring with own configure!" + CXXFLAGS=$(CXXFLAGS) ./configure --prefix=/usr + touch $@ + +build build-arch: build-stamp +build-stamp: configure-stamp + dh_testdir + echo "building with own build!" + $(MAKE) CXXFLAGS=$(CXXFLAGS) + touch $@ + +build-indep: + echo "Nothing to do for build-indep" + +binary-common: + dh_testdir + dh_testroot + dh_installchangelogs + dh_installdocs + dh_installexamples + dh_installman + dh_link + dh_strip + dh_compress -X.pdf + dh_fixperms + dh_makeshlibs + dh_installdeb + dh_shlibdeps + dh_gencontrol + dh_md5sums + dh_builddeb + +install install-arch: build-stamp + +install-indep: + echo Nothing to do for install-indep + +binary-indep: + #$(MAKE) -f debian/rules DH_OPTIONS=-i binary-common + echo Nothing to do for binary-indep + +binary-arch: build-arch + $(MAKE) -f debian/rules DH_OPTIONS=-s binary-common + +binary: binary-arch binary-indep + +clean: + dh_testdir + dh_testroot + find . -name "*.o" | xargs -r rm + dh_clean build-arch-stamp build-indep-stamp configure-stamp + + + + +VERSION=1.9+`date +"%Y%m%d"` +get-orig-source: + cvs -z3 -d:pserver:[email protected]:/cvsroot/gentle-m co -P GENtle + mv gentle gentle-$(VERSION) + tar --exclude CVS --exclude .cvsignore -cvf gentle_$(VERSION).orig.tar.gz gentle-$(VERSION) Property changes on: trunk/packages/gentle/trunk/debian/rules ___________________________________________________________________ Added: svn:executable + * _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/mailman/listinfo/debian-med-commit
