[med-svn] r15114 - trunk/packages/sibsim4/trunk/debian

Tue Nov 5 19:50:22 UTC 2013

Author: tille
Date: 2013-11-05 19:50:22 +0000 (Tue, 05 Nov 2013)
New Revision: 15114

Added:
   trunk/packages/sibsim4/trunk/debian/README.Debian
Modified:
   trunk/packages/sibsim4/trunk/debian/changelog
   trunk/packages/sibsim4/trunk/debian/copyright
Log:
DEP5; Add some historic notes about the origin to README.Debian where this information belongs to


Added: trunk/packages/sibsim4/trunk/debian/README.Debian
===================================================================

--- trunk/packages/sibsim4/trunk/debian/README.Debian	                        (rev 0)
+++ trunk/packages/sibsim4/trunk/debian/README.Debian	2013-11-05 19:50:22 UTC (rev 15114)
@@ -0,0 +1,25 @@
+SIBsim4 for Debian
+==================
+
+The SIBsim4 project is based on sim4[1], which is a program designed to
+align an expressed DNA sequence with a genomic sequence, allowing for
+introns. Sim4 was written by Liliana Florea while working in Webb
+Miller's lab at the Pennsylvania State University. Here is the paper[2]
+describing sim4 (source code is also available).
+
+The name was chosen to denote the fact the SIBsim4 is a derivative work
+from sim4. SIB[3] stands for the Swiss Institute of Bioinformatics. Some
+code modifications were written by Claudio Lottaz, while working at SIB.
+SIBsim4 is currently developed and maintained by Christian Iseli, from
+the Ludwig Institute for Cancer Research LICR[4], Information Technology
+Office in Lausanne. LICR is a SIB partner.
+
+[1] http://globin.cse.psu.edu/html/docs/sim4.html
+[2] http://www.genome.org/cgi/content/full/8/9/967
+    L. Florea, G. Hartzell, Z. Zhang, G. Rubin, and W. Miller (1998)
+    "A computer program for aligning a cDNA sequence with a genomic DNA sequence."
+    Genome Research 8, 967-974.
+[3] http://www.isb-sib.ch/
+[4] http://www.licr.org/
+
+ -- Andreas Tille <tille at debian.org>  Tue, 05 Nov 2013 18:43:45 +0100

Modified: trunk/packages/sibsim4/trunk/debian/changelog
===================================================================
--- trunk/packages/sibsim4/trunk/debian/changelog	2013-11-05 19:34:16 UTC (rev 15113)
+++ trunk/packages/sibsim4/trunk/debian/changelog	2013-11-05 19:50:22 UTC (rev 15114)
@@ -5,6 +5,9 @@
      - canonical Vcs URLs
      - debhelper 7
   * debian/rules: cdbs -> dh
+  * debian/README.Debian: Took over some information from debian/copyright
+    which actually belongs here
+  * debian/copyright: DEP5
 
  -- Andreas Tille <tille at debian.org>  Tue, 05 Nov 2013 18:43:45 +0100
 

Modified: trunk/packages/sibsim4/trunk/debian/copyright
===================================================================
--- trunk/packages/sibsim4/trunk/debian/copyright	2013-11-05 19:34:16 UTC (rev 15113)
+++ trunk/packages/sibsim4/trunk/debian/copyright	2013-11-05 19:50:22 UTC (rev 15114)
@@ -1,44 +1,34 @@
-This package was debianized by Nelson A. de Oliveira <naoliv at debian.org> on
-Wed, 10 Jan 2007 02:13:20 -0200.
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: SIBsim4
+Upstream-Contact: Christian Iseli <Christian.Iseli at licr.org>
+Source: http://sourceforge.net/projects/sibsim4/files/
 
-It was downloaded from http://sourceforge.net/projects/sibsim4/
+Files: *
+Copyright: © 2001-2010 Christian Iseli <Christian.Iseli at licr.org>,
+                       Claudio Lottaz
+                       Swiss Institute of Bioinformatics, and Ludwig
+                       Institute for Cancer Research (LICR)
+License: GPL2+
 
-Upstream Authors: Christian Iseli <Christian.Iseli at licr.org>
-		  Claudio Lottaz
-
-Copyright: 2001-2006 Swiss Institute of Bioinformatics, and Ludwig Institute
-	   for Cancer Research (LICR)
-
-This package implements the Sim4 algorithm for aligning expressed DNA
-with genomic sequences, described in the paper:
-
-L. Florea, G. Hartzell, Z. Zhang, G. Rubin, and W. Miller (1998)
-"A computer program for aligning a cDNA sequence with a genomic DNA sequence."
-Genome Research 8, 967-974.
-
-Portions copyright by:
-
-Copyright (C) 1998-2001  Liliana Florea
-Copyright (C) 1998-2001  Scott Schwartz
-
-License:
-
+License: GPL2+
    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
    (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 package; if not, write to the Free Software
    Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA  02110-1301 USA
+ .
+ On Debian systems, the complete text of the GNU General
+ Public License can be found in `/usr/share/common-licenses/GPL-2'.
 
-On Debian systems, the complete text of the GNU General
-Public License can be found in `/usr/share/common-licenses/GPL'.
-
-The Debian packaging is (C) 2007, Nelson A. de Oliveira <naoliv at debian.org> and
-is licensed under the GPL, see above.
+Files: debian/*
+Copyright: © 2007-2008 Nelson A. de Oliveira <naoliv at debian.org>
+           © 2010-2012 Andreas Tille <tille at debian.org>
+License: GPL2+


