[med-svn] r11017 - in trunk/packages: . ngila ngila/trunk ngila/trunk/debian

[Andreas Tille]

Author: tille
Date: 2012-05-27 07:01:02 +0000 (Sun, 27 May 2012)
New Revision: 11017

Added:
   trunk/packages/ngila/
   trunk/packages/ngila/trunk/
   trunk/packages/ngila/trunk/debian/
   trunk/packages/ngila/trunk/debian/changelog
   trunk/packages/ngila/trunk/debian/compat
   trunk/packages/ngila/trunk/debian/control
   trunk/packages/ngila/trunk/debian/copyright
   trunk/packages/ngila/trunk/debian/rules
   trunk/packages/ngila/trunk/debian/upstream
Log:
Inject information from task file and WNPP bug


Added: trunk/packages/ngila/trunk/debian/changelog
===================================================================
--- trunk/packages/ngila/trunk/debian/changelog	                        (rev 0)
+++ trunk/packages/ngila/trunk/debian/changelog	2012-05-27 07:01:02 UTC (rev 11017)
@@ -0,0 +1,5 @@
+ngila (1.3-1) unstable; urgency=low
+
+  * Initial release (Closes: #439996)
+
+ -- Andreas Tille <tille at debian.org>  Sun, 27 May 2012 08:49:50 +0200

Added: trunk/packages/ngila/trunk/debian/compat
===================================================================
--- trunk/packages/ngila/trunk/debian/compat	                        (rev 0)
+++ trunk/packages/ngila/trunk/debian/compat	2012-05-27 07:01:02 UTC (rev 11017)
@@ -0,0 +1 @@
+9

Added: trunk/packages/ngila/trunk/debian/control
===================================================================
--- trunk/packages/ngila/trunk/debian/control	                        (rev 0)
+++ trunk/packages/ngila/trunk/debian/control	2012-05-27 07:01:02 UTC (rev 11017)
@@ -0,0 +1,31 @@
+Source: ngila
+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://scit.us/projects/ngila/
+Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/ngila/trunk/
+Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/ngila/trunk/
+
+Package: ngila
+Architecture: any
+Depends: ${shlibs:Depends}, ${misc:Depends}
+Description: global pairwise alignments with logarithmic and affine gap costs
+ Ngila is an application that will find the best alignment of a pair
+ of sequences using log-affine gap costs, which are the most
+ biologically realistic gap costs.
+ .
+ Ngila implements the Miller and Myers (1988) algorithm in order to
+ find a least costly global alignment of two sequences given homology
+ costs and a gap cost. Two versions of the algorithm are
+ included: holistic and divide-and-conquer. The former is faster but
+ the latter utilizes less memory. Ngila starts with the
+ divide-and-conquer method but switches to the holistic method for
+ subsequences smaller than a user-established threshold. This improves
+ its speed without substantially increasing memory requirements. Ngila
+ also allows users to assign costs to end gaps that are smaller than
+ costs for internal gaps. This is important for aligning using the
+ free-end-gap method.

Added: trunk/packages/ngila/trunk/debian/copyright
===================================================================
--- trunk/packages/ngila/trunk/debian/copyright	                        (rev 0)
+++ trunk/packages/ngila/trunk/debian/copyright	2012-05-27 07:01:02 UTC (rev 11017)
@@ -0,0 +1,10 @@
+Format: http://www.debian.org/doc/packaging-manuals/copyright-format/1.0/
+Source: http://scit.us/projects/ngila/downloads
+
+Files: *
+Copyright: © 2008-2011 Reed A. Cartwright <racartwright at rice.edu>
+License: GPLv3
+
+Files: debian/*
+Copyright: © 2012 Andreas Tille <tille at debian.org>
+License: GPLv3

Added: trunk/packages/ngila/trunk/debian/rules
===================================================================
--- trunk/packages/ngila/trunk/debian/rules	                        (rev 0)
+++ trunk/packages/ngila/trunk/debian/rules	2012-05-27 07:01:02 UTC (rev 11017)
@@ -0,0 +1,6 @@
+#!/usr/bin/make -f
+
+# DH_VERBOSE := 1
+
+%:
+	dh $@


Property changes on: trunk/packages/ngila/trunk/debian/rules
___________________________________________________________________
Added: svn:executable
   + *

Added: trunk/packages/ngila/trunk/debian/upstream
===================================================================
--- trunk/packages/ngila/trunk/debian/upstream	                        (rev 0)
+++ trunk/packages/ngila/trunk/debian/upstream	2012-05-27 07:01:02 UTC (rev 11017)
@@ -0,0 +1,12 @@
+Reference:
+  Author: Reed A. Cartwright
+  Title: "Ngila: global pairwise alignments with logarithmic and affine gap costs"
+  Journal: Bioinformatics
+  Year: 2007
+  Volume: 23
+  Number: 11
+  Pages: 1427-1428
+  DOI: 10.1093/bioinformatics/btm095
+  PMID: 17387111
+  URL: http://bioinformatics.oxfordjournals.org/content/23/11/1427
+  eprint: http://bioinformatics.oxfordjournals.org/content/23/11/1427.full.pdf+html