[med-svn] r5826 - trunk/packages/bowtie/trunk/debian
Andreas Tille
tille at alioth.debian.org
Sun Jan 30 15:52:23 UTC 2011
Author: tille
Date: 2011-01-30 15:52:20 +0000 (Sun, 30 Jan 2011)
New Revision: 5826
Modified:
trunk/packages/bowtie/trunk/debian/copyright
trunk/packages/bowtie/trunk/debian/get-orig-source
trunk/packages/bowtie/trunk/debian/rules
Log:
Final polishing in copyright file; check whether Debian packaged version of SeqAn would work but failed and documented this issue in the code
Modified: trunk/packages/bowtie/trunk/debian/copyright
===================================================================
--- trunk/packages/bowtie/trunk/debian/copyright 2011-01-30 15:15:03 UTC (rev 5825)
+++ trunk/packages/bowtie/trunk/debian/copyright 2011-01-30 15:52:20 UTC (rev 5826)
@@ -1,49 +1,23 @@
-This work was packaged for Debian by:
+Format: http://dep.debian.net/deps/dep5/
+Upstream-Name: Bowtie
+Upstream-Contact: Ben Langmead <blangmea at jhsph.edu>
+Source: http://sourceforge.net/projects/bowtie-bio/files/bowtie/
- Steffen Moeller <moeller at debian.org> on Thu, 25 Nov 2010 17:04:39 +0100
-
-It was downloaded from:
-
- http://bowtie-bio.sf.net
-
Files: *
-
-Upstream Authors:
-
- Ben Langmead <email?>
-
-Copyright:
-
- Copyright (C) 2009-2010 Ben Langmead
- Copyright (C) 2009-2010 C. Trapnell
- Copyright (C) 2009-2010 M. Pop
- Copyright (C) 2009-2010 Steven L. Salzberg
-
+Copyright: © 2009-2010 Ben Langmead, C. Trapnell, M. Pop, Steven L. Salzberg
License:
-
This program is free software; you can redistribute it and/or modify it
under the terms of the "Artistic License" which comes with Debian.
THIS PACKAGE IS PROVIDED "AS IS" AND WITHOUT ANY EXPRESS OR IMPLIED
WARRANTIES, INCLUDING, WITHOUT LIMITATION, THE IMPLIED WARRANTIES
OF MERCHANTIBILITY AND FITNESS FOR A PARTICULAR PURPOSE.
+
+ On Debian systems, the complete text of the Artistic License
+ can be found in "/usr/share/common-licenses/Artistic".
-Publication:
-
- It is not a requirement of the license, but when you use this
- package for your research, you should cite
-
- Langmead B, Trapnell C, Pop M, Salzberg SL.
- Ultrafast and memory-efficient alignment of short DNA
- sequences to the human genome. Genome Biology 10:R25.
-
-On Debian systems, the complete text of the Artistic License
-can be found in "/usr/share/common-licenses/Artistic".
-
Files: SeqAn-1.1
-
Upstream Authors:
-
Andreas Döring <doering at inf.fu-berlin.de>
David Weese <weese at inf.fu-berlin.de>
Tobias Rausch <rausch at inf.fu-berlin.de>
@@ -52,19 +26,14 @@
Carsten Kemena <kemena at inf.fu-berlin.de>
Konrad Ludwig Moritz Rudolph <krudolph at inf.fu-berlin.de>
Marcel H. Schulz. <marcel.schulz at molgen.mpg.de>
-
Copyright:
-
If not otherwise stated Copyright (C) 2007-2009 the Seqan authors.
-
-
License:
-
This library is free software; you can redistribute it and/or
modify it under the terms of the GNU Lesser General Public
License as published by the Free Software Foundation; either
version 3 of the License, or (at your option) any later version.
-
+
This library 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
@@ -73,14 +42,11 @@
On Debian systems, you can find the LGPL license in:
/usr/share/common-licenses/LGPL
-
-File: SeqAn-1.1/seqan/index/index_sa_lss.h
-
+File: SeqAn-1.1/seqan/index/index_sa_lss.h
Copyright:
-
Copyright 1999 N. Jesper Larsson <jesper at cs.lth.se>
Copyright 2007 David Weese.
-
+License:
This software may be used freely for any purpose. However, when
distributed, the original source must be clearly stated, and, when
the source code is distributed, the copyright notice must be retained
@@ -88,9 +54,10 @@
is given regarding the quality of this software.
-The Debian packaging is:
-
- Copyright (C) 2010 Steffen Moeller <moeller at debian.org>
-
-and is licensed under the same license.
-
+Files: debian/*
+Copyright: © 2010 Files: *
+Copyright: © 2011 Steffen Moeller <moeller at debian.org>,
+ Yask Gupta <yask.gupta87 at gmail.com>
+ © 2011 Andreas Tille <tille at debian.org>
+License: PD
+ The packaging work is in the public domain unless stated otherwise.
Modified: trunk/packages/bowtie/trunk/debian/get-orig-source
===================================================================
--- trunk/packages/bowtie/trunk/debian/get-orig-source 2011-01-30 15:15:03 UTC (rev 5825)
+++ trunk/packages/bowtie/trunk/debian/get-orig-source 2011-01-30 15:52:20 UTC (rev 5826)
@@ -13,6 +13,10 @@
UPSTREAMDIR=${PKG}-${VERSION}
unzip ../"${UPSTREAMDIR}-src.zip"
+## remove copy of SeqAn library - unfortunately the package does not compile
+## with the Debian packaged version 1.2
+#rm -rf "${UPSTREAMDIR}"/SeqAn-1.1
+
GZIP="--best --no-name" tar -czf "$PKG"_"$VERSION".orig.tar.gz "${UPSTREAMDIR}"
rm -rf "${UPSTREAMDIR}"
Modified: trunk/packages/bowtie/trunk/debian/rules
===================================================================
--- trunk/packages/bowtie/trunk/debian/rules 2011-01-30 15:15:03 UTC (rev 5825)
+++ trunk/packages/bowtie/trunk/debian/rules 2011-01-30 15:52:20 UTC (rev 5826)
@@ -1,10 +1,7 @@
#!/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.
+# debian/rules for bowtie
+# Andreas Tille <tille at debian.org>
+# GPL
# Uncomment this to turn on verbose mode.
#export DH_VERBOSE=1
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