[med-svn] [SCM] bowtie2 branch, master, updated. upstream/2.0.0-beta5-8-g2e113a6

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 1c63e02dccb400fd7cc8e61c4e8783950aafa036
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Wed Feb 22 08:42:40 2012 +0100

    Fixed minor linitan complains , added ls.h to debain/copyright
    License is GPL3 and not GPL2.
    Added manual page name generation command in debian/rules
    Added override_dh_installchangelogs to install NEWS as the changelog

diff --git a/debian/changelog b/debian/changelog
index 4cbb8f2..6afc9ff 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -2,4 +2,4 @@ bowtie2 (2.0.0-beta5-1) UNRELEASED; urgency=low
 
   * Initial release (Closes: #660762)
 
- -- Alex Mestiashvili <alex at biotec.tu-dresden.de>  Tue, 21 Feb 2012 18:51:53 +0100
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Tue, 21 Feb 2012 18:51:53 +0100
diff --git a/debian/control b/debian/control
index 5aeae0d..f6d2f12 100644
--- a/debian/control
+++ b/debian/control
@@ -1,12 +1,14 @@
 Source: bowtie2
 Section: science
 Priority: extra
-Maintainer:  Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
 DM-Upload-Allowed: yes
 Uploaders: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
 Build-Depends: debhelper (>= 8.0), help2man
 Standards-Version: 3.9.2
 Homepage: http://bowtie-bio.sourceforge.net/bowtie2
+Vcs-Browser: http://git.debian.org/?p=debian-med/bowtie2.git
+Vcs-Git: git://git.debian.org/debian-med/bowtie2.git
 
 Package: bowtie2
 Architecture: any
diff --git a/debian/copyright b/debian/copyright
index db63668..8c3c1fe 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -5,26 +5,29 @@ Source: http://sourceforge.net/projects/bowtie2-bio/files/bowtie2/
 
 Files: *
 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.
+License: GPL-3.0+
 
-    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".
+Files: ls.h
+Copyright: © 1999, N. Jesper Larsson
+License:
+ This file contains an implementation of the algorithm presented in "Faster
+ Suffix Sorting" by N. Jesper Larsson (jesper at cs.lth.se) and Kunihiko
+ Sadakane (sada at is.s.u-tokyo.ac.jp).
+ .
+ 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.
 
 Files: debian/*
-Copyright: © 2010 Files: *
-Copyright: © 2012 Alex Mestiashvili <alex at biotec.tu-dresden.de>
-License: GPL-2.0+
+Copyright: © 2012 Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
+License: GPL-3.0+
 
-License: GPL-2.0+
+License: GPL-3.0+
  This package 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
+ 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,
@@ -36,4 +39,4 @@ License: GPL-2.0+
  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 2 can be found in "/usr/share/common-licenses/GPL-2".
+ Public License version 3 can be found in "/usr/share/common-licenses/GPL-3".
diff --git a/debian/rules b/debian/rules
index 955b638..2fa237f 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,21 +1,26 @@
 #!/usr/bin/make -f
 
-pkg=bowtie2
+pkg=$(shell dpkg-parsechangelog | sed -n 's/^Source: //p')
 
 %:
 	dh $@
 
 override_dh_auto_install:
 	mkdir -p $(CURDIR)/debian/$(pkg)/usr/share/man/man1/
-	for bin in bowtie2 bowtie2-build bowtie2-inspect bowtie2-align; do \
-	    help2man $(CURDIR)/$${bin} > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$${bin}.1 ; \
-	done
-	help2man --name="ultrafast memory-efficient short read aligner" --no-info \
+#	for bin in bowtie2 bowtie2-build bowtie2-inspect bowtie2-align; do \
+#	    help2man $(CURDIR)/$${bin} > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/$${bin}.1 ; \
+#	done
+	help2man --name="wrapper for bowtie2-align" --no-info \
              $(CURDIR)/bowtie2 > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie2.1
-	help2man --name="building a colorspace index for bowtie2" --no-info \
+	help2man --name="builds a Bowtie index from a set of DNA sequences" --no-info \
              $(CURDIR)/bowtie2-build > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie2-build.1
 	help2man --name="extracts information from a bowtie2 index" --no-info \
              $(CURDIR)/bowtie2-inspect > $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie2-inspect.1
+	help2man --name="ultrafast and memory-efficient tool for aligning sequencing reads to long reference sequences" --no-info \
+             $(CURDIR)/bowtie2-align> $(CURDIR)/debian/$(pkg)/usr/share/man/man1/bowtie2-align.1
+
+override_dh_installchangelogs:
+        dh_installchangelogs NEWS
 
 get-orig-source:
 	. debian/get-orig-source

-- 
ultrafast memory-efficient short read aligner