[med-svn] [SCM] tophat branch, master, updated. debian/2.0.6-1-18-gb16c75d

Thu Jul 4 15:04:56 UTC 2013

The following commit has been merged in the master branch:
commit 94158df4d7b53d7d384c94241041fe0a3b9b3609
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Jul 4 14:39:54 2013 +0200

     - d/copyright: updated years and added new files
     - d/control: removed obsoleted DM-Upload-Allowed

diff --git a/debian/control b/debian/control
index d6e0546..c37bc4a 100644
--- a/debian/control
+++ b/debian/control
@@ -2,7 +2,6 @@ Source: tophat
 Section: science
 Priority: optional
 Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
-DM-Upload-Allowed: yes
 Uploaders: Carlos Borroto <carlos.borroto at gmail.com>,
  Alexandre Mestiashvili <alex at biotec.tu-dresden.de>,
  Andreas Tille <tille at debian.org>
diff --git a/debian/copyright b/debian/copyright
index 94fa861..911e21e 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,7 +1,7 @@
 Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
 Upstream-Name: TopHat
 Upstream-Contact: Cole Trapnell <cole at cs.umd.edu>
-Source: http://tophat.cbcb.umd.edu/downloads/tophat-2.0.8b.tar.gz
+Source: http://tophat.cbcb.umd.edu/downloads/tophat-2.0.9.tar.gz
 Comment:
  Cole Trapnell wrote TopHat. TopHat is built on Bowtie, which was written by
  Ben Langmead and Cole Trapnell.  Daehwan Kim and Geo Pertea added support
@@ -16,44 +16,88 @@ License: Artistic
 Files: ax_bam.m4
 Copyright: © 2010 Cole Trapnell <cole at cs.umd.edu>
 License: GAP
- Copying and distribution of this file, with or without modification, are
- permitted in any medium without royalty provided the copyright notice
- and this notice are preserved.
 
-Files: ax_check_zlib.m4
-Copyright: © 2008 Loic Dachary <loic at senga.org>
-License: GPL-2+ with autoconf exception
- 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.
+Files: ax_boost_thread.m4
+Copyright: © 2009 Thomas Porschberg <thomas at randspringer.de>
+           © 2009 Michael Tindal
+License: GAP
+
+Files: ax_boost_base.m4
+Copyright: © 2009 Thomas Porschberg <thomas at randspringer.de>
+License: GAP
+
+Files: build-aux/*
+Copyright: © 1994-2005 Free Software Foundation, Inc.
+License: GPL-2+ with Autoconf exception
+ This file 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 St, Fifth Floor, Boston, 
+ MA 02110-1301, USA.
  .
- 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.
+ As a special exception to the GNU General Public License, if you
+ distribute this file as part of a program that contains a
+ configuration script generated by Autoconf, you may include it under
+ the same distribution terms that you use for the rest of that program.
+
+Files: build-aux/install-sh
+Copyright: © 1994 X Consortium
+License: 
+ 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:
  .
- You should have received a copy of the GNU General Public License along
- with this program. If not, see <http://www.gnu.org/licenses/>.
+ The above copyright notice and this permission notice shall be included in
+ all copies or substantial portions of the Software.
  .
- As a special exception, the respective Autoconf Macro's copyright owner
- gives unlimited permission to copy, distribute and modify the configure
- scripts that are the output of Autoconf when processing the Macro. You
- need not follow the terms of the GNU General Public License when using
- or distributing such scripts, even though portions of the text of the
- Macro appear in them. The GNU General Public License (GPL) does govern
- all other use of the material that constitutes the Autoconf Macro.
+ 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
+ X CONSORTIUM BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN
+ AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNEC-
+ TION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
  .
- This special exception to the GPL applies to versions of the Autoconf
- Macro released by the Autoconf Archive. When you make and distribute a
- modified version of the Autoconf Macro, you may extend this special
- exception to the GPL to apply to your modified version as well.
+ Except as contained in this notice, the name of the X Consortium shall not
+ be used in advertising or otherwise to promote the sale, use or other deal-
+ ings in this Software without prior written authorization from the X Consor-
+ tium.
+Comment: FSF changes to this file are in the public domain.
+
+Files: aclocal.m4
+Copyright: © 1996-2005 Free Software Foundation, Inc.
+License:
+ This file is free software; the Free Software Foundation
+ gives unlimited permission to copy and/or distribute it,
+ with or without modifications, as long as this notice is preserved.
+
+Files: INSTALL configure
+Copyright: © 1992-2010 Free Software Foundation, Inc.
+License:
+ This configure script is free software; the Free Software Foundation
+ gives unlimited permission to copy, distribute and modify it.
 
 Files: debian/*
-Copyright: 2011 Carlos Borroto <carlos.borroto at gmail.com>
-           © 2011 Alex Mestiashvili <alex at biotec.tu-dresden.de>
+Copyright: © 2011 Carlos Borroto <carlos.borroto at gmail.com>
+           © 2013 Alex Mestiashvili <alex at biotec.tu-dresden.de>
 License: GPL-2+
 
+License: GAP
+ Copying and distribution of this file, with or without modification, are
+ permitted in any medium without royalty provided the copyright notice
+ and this notice are preserved.
+
 License: Artistic
  This program is free software; you can redistribute it and/or modify
  it under the terms of the Artistic License, which comes with Perl.

-- 
A spliced read mapper for RNA-Seq

