[med-svn] r4839 - in trunk/packages: . gentle gentle/trunk gentle/trunk/debian
Steffen Möller
moeller at alioth.debian.org
Tue May 25 23:19:48 UTC 2010
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 <moeller at debian.org> 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 <moeller at debian.org> 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 <moeller at debian.org>
+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 <moeller at debian.org> on Tue, 09 Mar 2010 10:42:41 +0100
+
+It was downloaded from:
+
+ http://gentle.magnusmanske.de/
+
+Files: clustalw/*
+
+Upstream Authors:
+ Toby J. Gibson <gibson at embl-heidelberg.de>
+ J. D. Thompson <thompson at igbmc.u-strasbg.fr>
+ Des G. Higgins <d.higgins at ucc.ie>
+
+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:-
+ gibson at embl-heidelberg.de
+ thompson at igbmc.u-strasbg.fr
+ d.higgins at ucc.ie
+
+
+ ******************************************************************************
+
+ 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 <magnusmanske+gentle at googlemail.com>
+
+Copyright:
+ Magnus Manske <magnusmanske+gentle at googlemail.com>
+
+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 <moeller at debian.org>
+
+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 <moeller at debian.org>,
+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
+ $(MAKE) -f debian/rules DH_OPTIONS=-s binary-common
+
+binary: binary-arch binary-indep
+
+clean:
+ dh_testdir
+ dh_testroot
+ find . -name "*.o" | xargs -r rm
+ dh_clean build-arch-stamp build-indep-stamp configure-stamp
+
+
+
+
+VERSION=1.9+`date +"%Y%m%d"`
+get-orig-source:
+ cvs -z3 -d:pserver:anonymous at gentle-m.cvs.sourceforge.net:/cvsroot/gentle-m co -P GENtle
+ mv gentle gentle-$(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
+ *
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