[med-svn] r11001 - in trunk/packages: . logomat-m logomat-m/trunk logomat-m/trunk/debian

[Andreas Tille]

Author: tille
Date: 2012-05-25 11:48:20 +0000 (Fri, 25 May 2012)
New Revision: 11001

Added:
   trunk/packages/logomat-m/
   trunk/packages/logomat-m/trunk/
   trunk/packages/logomat-m/trunk/debian/
   trunk/packages/logomat-m/trunk/debian/changelog
   trunk/packages/logomat-m/trunk/debian/compat
   trunk/packages/logomat-m/trunk/debian/control
   trunk/packages/logomat-m/trunk/debian/copyright
   trunk/packages/logomat-m/trunk/debian/upstream
Log:
Inject data from med-bio task file as machine readable packaging files to enable machine-readable gatherer fetching it


Added: trunk/packages/logomat-m/trunk/debian/changelog
===================================================================
--- trunk/packages/logomat-m/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/changelog	2012-05-25 11:48:20 UTC (rev 11001)
@@ -0,0 +1,5 @@
+logomat-m (0.0.20091119-1) unstable; urgency=low
+
+  * Initial release
+
+ -- Andreas Tille <tille at debian.org>  Thu, 24 May 2012 14:30:13 +0200

Added: trunk/packages/logomat-m/trunk/debian/compat
===================================================================
--- trunk/packages/logomat-m/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/compat	2012-05-25 11:48:20 UTC (rev 11001)
@@ -0,0 +1 @@
+9

Added: trunk/packages/logomat-m/trunk/debian/control
===================================================================
--- trunk/packages/logomat-m/trunk/debian/control	                        (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/control	2012-05-25 11:48:20 UTC (rev 11001)
@@ -0,0 +1,27 @@
+Source: logomat-m
+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 (>= 9)
+Standards-Version: 3.9.3
+Homepage: http://www.sanger.ac.uk/resources/software/logomat-m/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/logomat-m/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/logomat-m/trunk/
+
+Package: logomat-m
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: visualize central aspects of Profile Hidden Markov Models (pHMMs)
+ Profile Hidden Markov Models (pHMMs) are a widely used tool for
+ protein family research. We present a method to visualize all of
+ their central aspects graphically, thus generalizing the concept of
+ sequence logos introduced by Schneider and Stephens. For each
+ emitting state of the pHMM, we display a stack of letters. As for
+ sequence logos, the stack height is determined by the deviation of
+ the position's letter emission frequencies from the background
+ frequencies of the letters. As a new feature, the stack width now
+ visualizes both the probability of reaching the state (the hitting
+ probability) and the expected number of letters the state emits
+ during a pass through the model (the expected contribution).

Added: trunk/packages/logomat-m/trunk/debian/copyright
===================================================================
--- trunk/packages/logomat-m/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/copyright	2012-05-25 11:48:20 UTC (rev 11001)
@@ -0,0 +1,11 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Upstream-Name: LogoMat-M
+Source: ftp://ftp.sanger.ac.uk/pub4/resources/software/logomat-m/
+
+Files: *
+Copyright: © -2009 ???
+License: Artistic
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille at debian.org>
+License: Artistic

Added: trunk/packages/logomat-m/trunk/debian/upstream
===================================================================
--- trunk/packages/logomat-m/trunk/debian/upstream	                        (rev 0)
+++ trunk/packages/logomat-m/trunk/debian/upstream	2012-05-25 11:48:20 UTC (rev 11001)
@@ -0,0 +1,11 @@
+Reference:
+  Author: Benjamin Schuster-Böckler and Jörg Schultz and Sven Rahmann
+  Title: HMM Logos for visualization of protein families
+  Journal: BMC Bioinformatics
+  Year: 2004
+  Volume: 5
+  Pages: 7
+  DOI: 10.1186/1471-2105-5-7
+  PMID: 14736340
+  URL: http://www.biomedcentral.com/1471-2105/5/7
+  eprint: http://www.biomedcentral.com/content/pdf/1471-2105-5-7.pdf