[med-svn] r5950 - in trunk/packages: . abacas abacas/trunk abacas/trunk/debian abacas/trunk/debian/source

[Andreas Tille]

Author: tille
Date: 2011-02-11 13:54:51 +0000 (Fri, 11 Feb 2011)
New Revision: 5950

Added:
   trunk/packages/abacas/
   trunk/packages/abacas/trunk/
   trunk/packages/abacas/trunk/debian/
   trunk/packages/abacas/trunk/debian/changelog
   trunk/packages/abacas/trunk/debian/compat
   trunk/packages/abacas/trunk/debian/control
   trunk/packages/abacas/trunk/debian/copyright
   trunk/packages/abacas/trunk/debian/source/
   trunk/packages/abacas/trunk/debian/source/format
   trunk/packages/abacas/trunk/debian/watch
Log:
Quick shot at abacas packaging.  Packaging technical it seems to be a very easy target.  It's used in our institute.  Anybody willing to complete this task?


Added: trunk/packages/abacas/trunk/debian/changelog
===================================================================
--- trunk/packages/abacas/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/abacas/trunk/debian/changelog	2011-02-11 13:54:51 UTC (rev 5950)
@@ -0,0 +1,6 @@
+abacas (1.3.1-1) unstable; urgency=low
+
+  * Initial release (Closes: #????)
+  PACKAGING NOT FINISHED - FEEL FREE TO TAKE OVER
+
+ -- Andreas Tille <tille at debian.org>  Mon, 11 Feb 2011 12:02:43 +0100

Added: trunk/packages/abacas/trunk/debian/compat
===================================================================
--- trunk/packages/abacas/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/abacas/trunk/debian/compat	2011-02-11 13:54:51 UTC (rev 5950)
@@ -0,0 +1 @@
+7

Added: trunk/packages/abacas/trunk/debian/control
===================================================================
--- trunk/packages/abacas/trunk/debian/control	                        (rev 0)
+++ trunk/packages/abacas/trunk/debian/control	2011-02-11 13:54:51 UTC (rev 5950)
@@ -0,0 +1,29 @@
+Source: abacas
+Section: science
+Priority: optional
+Maintainer: Debian Med Packaging Team <debian-med-packaging at lists.alioth.debian.org>
+DM-Upload-Allowed: yes
+Uploaders: Andreas Tille <tille at debian.org>
+Build-Depends: debhelper (>= 7.1)
+Standards-Version: 3.9.1
+Homepage: http://abacas.sourceforge.net/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/abacas/trunk/?rev=0&sc=0
+Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/abacas/trunk/
+
+Package: abacas
+Architecture: all
+Depends: ${perl:Depends}, ${misc:Depends}, mummer
+Description: Algorithm Based Automatic Contiguation of Assembled Sequences
+ ABACAS is intended to rapidly contiguate (align, order, orientate),
+ visualize and design primers to close gaps on shotgun assembled contigs
+ based on a reference sequence.
+ .
+ ABACAS uses MUMmer to find alignment positions and identify syntenies
+ of assembled contigs against the reference. The output is then processed
+ to generate a pseudomolecule taking overlapping contigs and gaps in to
+ account. ABACAS generates a comparision file that can be used to
+ visualize ordered and oriented contigs in ACT. Synteny is represented by
+ red bars where colour intensity decreases with lower values of percent
+ identity between comparable blocks. Information on contigs such as the
+ orientation, percent identity, coverage and overlap with other contigs
+ can also be visualized by loading the outputted feature file on ACT.

Added: trunk/packages/abacas/trunk/debian/copyright
===================================================================
--- trunk/packages/abacas/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/abacas/trunk/debian/copyright	2011-02-11 13:54:51 UTC (rev 5950)
@@ -0,0 +1,29 @@
+Machine-readable license summary, see ‘http://dep.debian.net/deps/dep5/’.
+
+Name    :  Abacas
+Contact :  
+Source  :  http://sourceforge.net/projects/abacas/files/
+
+Copyright: © 2008-10 Genome Research Limited. All Rights Reserved.
+License: GPL-2+
+	
+	Abacas 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.
+	
+	Velvet 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 Velvet; 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 version 2 can be found in ‘/usr/share/common-licenses/GPL-2’.
+
+Files: debian/*
+Copyright: © 2011 Andreas Tille <tille at debian.org>
+License: Same as abacas

Added: trunk/packages/abacas/trunk/debian/source/format
===================================================================
--- trunk/packages/abacas/trunk/debian/source/format	                        (rev 0)
+++ trunk/packages/abacas/trunk/debian/source/format	2011-02-11 13:54:51 UTC (rev 5950)
@@ -0,0 +1 @@
+3.0 (quilt)

Added: trunk/packages/abacas/trunk/debian/watch
===================================================================
--- trunk/packages/abacas/trunk/debian/watch	                        (rev 0)
+++ trunk/packages/abacas/trunk/debian/watch	2011-02-11 13:54:51 UTC (rev 5950)
@@ -0,0 +1,2 @@
+version=3
+http://sf.net/abacas/abacas\.([\d\.]+)\.pl