[med-svn] [SCM] tophat branch, master, updated. upstream/1.3.3-5-g66e84fd

[Alexandre Mestiashvili]

The following commit has been merged in the master branch:
commit 66e84fd1a395c63fec896e36cf714a1467761e38
Author: Alexandre Mestiashvili <alex at biotec.tu-dresden.de>
Date:   Thu Dec 15 17:55:01 2011 +0100

    some cleanup in debian/* ;see debian/changelog for details

diff --git a/debian/changelog b/debian/changelog
index e25693d..321f3eb 100644
--- a/debian/changelog
+++ b/debian/changelog
@@ -1,8 +1,25 @@
 tophat (1.3.3-1) UNRELEASED; urgency=low
 
+  TODO:
+  * src/SeqAn-1.2 should be excluded
+    - tophat depends on seqan library which already exists in debian 
+  
+  [Alexandre Mestiashvili]
   * New upstream release 
-
- -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Thu, 15 Dec 2011 17:01:02 +0100
+  * Removed dh-make template from watch file
+  * Added initial copyright data , removed templates , added Source  
+  * debian/compat version 8
+  * debian/control 
+    - Maintainer: Debian Med Packaging Team
+      <debian-med-packaging at lists.alioth.debian.org>
+    - DM-Upload-Allowed: yes
+    - Added myself to Uploaders:
+    - added correct Vcs-Git , Vcs-Browser fields
+    - Standards-Version: 3.9.2
+  * debian/rules
+    - removed dh-make template 
+
+ -- Alexandre Mestiashvili <alex at biotec.tu-dresden.de>  Thu, 15 Dec 2011 17:51:47 +0100
 
 tophat (1.3.1-1ppa1~lucid1) lucid; urgency=low
 
diff --git a/debian/compat b/debian/compat
index 7f8f011..45a4fb7 100644
--- a/debian/compat
+++ b/debian/compat
@@ -1 +1 @@
-7
+8
diff --git a/debian/control b/debian/control
index 689f3cb..69d5628 100644
--- a/debian/control
+++ b/debian/control
@@ -1,12 +1,15 @@
 Source: tophat
 Section: science
 Priority: optional
-Maintainer: Carlos Borroto <carlos.borroto at gmail.com>
-Build-Depends: debhelper (>= 7.0.50~), autotools-dev, libbam-dev (>=0.1.16), zlib1g-dev
-Standards-Version: 3.9.1
+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>
+Build-Depends: debhelper (>= 8), autotools-dev, libbam-dev (>=0.1.16), zlib1g-dev
+Standards-Version: 3.9.2
 Homepage: http://tophat.cbcb.umd.edu/
-#Vcs-Git: git://git.debian.org/collab-maint/tophat.git
-#Vcs-Browser: http://git.debian.org/?p=collab-maint/tophat.git;a=summary
+Vcs-Git: git://git.debian.org/debian-med/tophat.git
+Vcs-Browser: http://git.debian.org/?p=debian-med/cufflinks.git;a=summary
 
 Package: tophat
 Architecture: any
diff --git a/debian/copyright b/debian/copyright
index e89ed1f..84e5da2 100644
--- a/debian/copyright
+++ b/debian/copyright
@@ -1,20 +1,25 @@
 Format: http://dep.debian.net/deps/dep5
 Upstream-Name: tophat
-Source: <url://example.com>
+Source: http://tophat.cbcb.umd.edu/downloads/tophat-1.3.3.tar.gz
 
 Files: *
-Copyright: <years> <put author's name and email here>
-           <years> <likewise for another author>
-License: <special license>
- <Put the license of the package here indented by 1 space>
- <This follows the format of Description: lines in control file>
- .
- <Including paragraphs>
+Copyright: Copyright: Copyright (C) 2003-2010 Cole Trapnell et al
+License: Artistic
 
-# If you want to use GPL v2 or later for the /debian/* files use 
-# the following clauses, or change it to suit. Delete these two lines
 Files: debian/*
 Copyright: 2011 Carlos Borroto <carlos.borroto at gmail.com>
+ © 2011 Alex Mestiashvili <alex at biotec.tu-dresden.de>
+License GPL-2+
+
+
+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.
+ .
+ On Debian systems, the complete text of the Artistic License can be
+ found in `/usr/share/common-licenses/Artistic'.
+
+
 License: GPL-2+
  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
@@ -31,6 +36,3 @@ License: GPL-2+
  .
  On Debian systems, the complete text of the GNU General
  Public License version 2 can be found in "/usr/share/common-licenses/GPL-2".
-
-# Please also look if there are files or directories which have a
-# different copyright/license attached and list them here.
diff --git a/debian/rules b/debian/rules
index b760bee..736b14e 100755
--- a/debian/rules
+++ b/debian/rules
@@ -1,10 +1,4 @@
 #!/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.
 
 # Uncomment this to turn on verbose mode.
 #export DH_VERBOSE=1

-- 
A spliced read mapper for RNA-Seq