[med-svn] r4180 - in trunk/packages/bwa/trunk: . debian

Charles Plessy plessy at alioth.debian.org
Wed Oct 7 05:13:24 UTC 2009 

Author: plessy
Date: 2009-10-07 05:13:24 +0000 (Wed, 07 Oct 2009)
New Revision: 4180

Added:
   trunk/packages/bwa/trunk/debian/
   trunk/packages/bwa/trunk/debian/changelog
   trunk/packages/bwa/trunk/debian/compat
   trunk/packages/bwa/trunk/debian/control
   trunk/packages/bwa/trunk/debian/copyright
   trunk/packages/bwa/trunk/debian/docs
   trunk/packages/bwa/trunk/debian/install
   trunk/packages/bwa/trunk/debian/manpages
   trunk/packages/bwa/trunk/debian/rules
   trunk/packages/bwa/trunk/debian/upstream-metadata.yaml
   trunk/packages/bwa/trunk/debian/watch
Log:
[svn-inject] Applying Debian modifications to trunk


Property changes on: trunk/packages/bwa/trunk/debian
___________________________________________________________________
Added: mergeWithUpstream
   + 1

Added: trunk/packages/bwa/trunk/debian/changelog
===================================================================
--- trunk/packages/bwa/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/bwa/trunk/debian/changelog	2009-10-07 05:13:24 UTC (rev 4180)
@@ -0,0 +1,5 @@
+bwa (0.5.3-1) UNRELEASED; urgency=low
+
+  * Initial release (Closes: #548719)
+
+ -- Charles Plessy <plessy at debian.org>  Mon, 28 Sep 2009 19:16:57 +0900

Added: trunk/packages/bwa/trunk/debian/compat
===================================================================
--- trunk/packages/bwa/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/bwa/trunk/debian/compat	2009-10-07 05:13:24 UTC (rev 4180)
@@ -0,0 +1 @@
+7

Added: trunk/packages/bwa/trunk/debian/control
===================================================================
--- trunk/packages/bwa/trunk/debian/control	                        (rev 0)
+++ trunk/packages/bwa/trunk/debian/control	2009-10-07 05:13:24 UTC (rev 4180)
@@ -0,0 +1,23 @@
+Source: bwa
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Charles Plessy <plessy at debian.org>
+Build-Depends: cdbs, debhelper (>= 7), zlib1g-dev
+Standards-Version: 3.8.3
+Homepage: http://bio-bwa.sourceforge.net/ 
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/bwa/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/bwa/trunk/
+
+Package: bwa
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Suggests: samtools
+Description: Burrows-Wheeler Aligner
+ Burrows-Wheeler Aligner (BWA) is a program that aligns relatively short
+ nucleotide sequences against a long reference sequence such as the human
+ genome. It implements two algorithms, bwa-short and dBWT-SW. The former works
+ for query sequences shorter than 200 bp and the latter for longer sequences up
+ to around 100 kbp. Both algorithms do gapped alignment. They are usually more
+ accurate and faster on queries with low error rates.

Added: trunk/packages/bwa/trunk/debian/copyright
===================================================================
--- trunk/packages/bwa/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/bwa/trunk/debian/copyright	2009-10-07 05:13:24 UTC (rev 4180)
@@ -0,0 +1,63 @@
+Name      :  Burrows-Wheeler Aligner
+Contact   :  bio-bwa-help at lists.sourceforge.net
+Source    :  http://downloads.sourceforge.net/project/bio-bwa/bwa-0.5.3.tar.bz2
+
+Copyright :  © 2008 Genome Research Ltd (GRL)
+             2008, by Heng Li <lh3 at sanger.ac.uk>
+             © 2003-2006, 2008, 2009, by Heng Li <lh3lh3 at gmail.com>
+             © 2008, by Attractive Chaos <attractivechaos at aol.co.uk>
+             © 2008 Yuta Mori
+License   :  MIT
+	
+	Permission is hereby granted, free of charge, to any person obtaining
+	a copy of this software and associated documentation files (the
+	"Software"), to deal in the Software without restriction, including
+	without limitation the rights to use, copy, modify, merge, publish,
+	distribute, sublicense, and/or sell copies of the Software, and to
+	permit persons to whom the Software is furnished to do so, subject to
+	the following conditions:
+	
+	The above copyright notice and this permission notice shall be
+	included in all copies or substantial portions of the Software.
+	
+	THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+	EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+	MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+	NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS
+	BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN
+	ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
+	CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+	SOFTWARE.
+
+
+Files     :  bwt_gen/bwt_gen.*
+Copyright :  © 2004, Wong Chi Kwong
+License   :  GPL-2+
+ 
+ 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 2 of the License, or
+ (at your option) any later version.
+ 
+ This program 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, write to the Free Software Foundation, Inc.,
+ 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
+
+On Debian systems, you can find a copy of the GNU General Public License
+version 2 in ‘/usr/share/common-licenses/GPL-2’.
+
+
+Files     :  bwt_gen/QSufSort.*
+Copyright :  1999, N. Jesper Larsson
+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 and any alterations in
+ the code must be clearly marked. No warranty is given regarding the quality
+ of this software.

Added: trunk/packages/bwa/trunk/debian/docs
===================================================================
--- trunk/packages/bwa/trunk/debian/docs	                        (rev 0)
+++ trunk/packages/bwa/trunk/debian/docs	2009-10-07 05:13:24 UTC (rev 4180)
@@ -0,0 +1,2 @@
+ChangeLog
+NEWS

Added: trunk/packages/bwa/trunk/debian/install
===================================================================
--- trunk/packages/bwa/trunk/debian/install	                        (rev 0)
+++ trunk/packages/bwa/trunk/debian/install	2009-10-07 05:13:24 UTC (rev 4180)
@@ -0,0 +1,3 @@
+bwa	usr/bin
+# A different solid2fastq.pl script is present in the maq package.
+solid2fastq.pl	usr/share/bwa

Added: trunk/packages/bwa/trunk/debian/manpages
===================================================================
--- trunk/packages/bwa/trunk/debian/manpages	                        (rev 0)
+++ trunk/packages/bwa/trunk/debian/manpages	2009-10-07 05:13:24 UTC (rev 4180)
@@ -0,0 +1 @@
+bwa.1

Added: trunk/packages/bwa/trunk/debian/rules
===================================================================
--- trunk/packages/bwa/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/bwa/trunk/debian/rules	2009-10-07 05:13:24 UTC (rev 4180)
@@ -0,0 +1,4 @@
+#!/usr/bin/make -f
+
+include /usr/share/cdbs/1/rules/debhelper.mk
+include /usr/share/cdbs/1/class/makefile.mk


Property changes on: trunk/packages/bwa/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/bwa/trunk/debian/upstream-metadata.yaml
===================================================================
--- trunk/packages/bwa/trunk/debian/upstream-metadata.yaml	                        (rev 0)
+++ trunk/packages/bwa/trunk/debian/upstream-metadata.yaml	2009-10-07 05:13:24 UTC (rev 4180)
@@ -0,0 +1,17 @@
+DOI: 10.1093/bioinformatics/btp324
+Homepage: http://bio-bwa.sourceforge.net/
+PMID: 19451168
+Reference: |
+ @article{HengLi07152009,
+ author = {Li, Heng and Durbin, Richard},
+ title = {{Fast and accurate short read alignment with Burrows-Wheeler transform}},
+ journal = {Bioinformatics},
+ volume = {25},
+ number = {14},
+ pages = {1754-1760},
+ doi = {10.1093/bioinformatics/btp324},
+ year = {2009},
+ URL = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/14/1754},
+ eprint = {http://bioinformatics.oxfordjournals.org/cgi/reprint/25/14/1754.pdf}
+}
+Repository: https://bio-bwa.svn.sourceforge.net/svnroot/bio-bwa

Added: trunk/packages/bwa/trunk/debian/watch
===================================================================
--- trunk/packages/bwa/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/bwa/trunk/debian/watch	2009-10-07 05:13:24 UTC (rev 4180)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/bio-bwa/bwa-(.*)\.tar\.bz2

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