[Blends-commit] r3366 - /projects/med/trunk/debian-med/tasks/bio

Sun May 27 07:17:21 UTC 2012

Author: tille
Date: Sun May 27 07:17:20 2012
New Revision: 3366

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3366
Log:
Strip now redundant information from task file

Modified:
    projects/med/trunk/debian-med/tasks/bio

Modified: projects/med/trunk/debian-med/tasks/bio
URL: http://svn.debian.org/wsvn/blends/projects/med/trunk/debian-med/tasks/bio?rev=3366&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Sun May 27 07:17:20 2012
@@ -363,9 +363,14 @@
 
 Depends: kempbasu
 
+Depends: lagan
+X-Category: Comparative genomics
+
 Depends: logomat-m
 
 Depends: molekel
+
+Depends: ngila
 
 Depends: pal2nal
 
@@ -585,31 +590,6 @@
 Remark: Successor for ssaha2 available: smalt
  The program smalt is from the same author is according to its author
  faster and more precise than ssaha2 (except for sequences > 2000bp)
-
-Depends: ngila
-Homepage: http://scit.us/projects/ngila/
-License: GPLv3
-Responsible: Charles Plessy <plessy at debian.org>
-WNPP: 439996
-Pkg-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.
- .
- Ngila is published in Cartwright RA Bioinformatics 2007
- 23(11):1427-1428; doi:10.1093/bioinformatics/btm095
 
 Depends: bio-mauve
 Homepage: http://asap.ahabs.wisc.edu/mauve/
@@ -2318,27 +2298,6 @@
  and part-of relations. Amongst the databases cureated by this tool
  is the GeneOntology.
 
-Depends: lagan
-Homepage: http://lagan.stanford.edu/lagan_web/index.shtml
-License: GPL
-Pkg-Description: highly parametrizable pairwise global alignment program
- Lagan takes local alignments generated by CHAOS as anchors, and limits the search area of
- the Needleman-Wunsch algorithm around these anchors.
- .
- Multi-LAGAN is a generalization of the pairwise algorithm to multiple sequence alignment.
- M-LAGAN performs progressive pairwise alignments, guided by a user-specified phylogenetic
- tree. Alignments are aligned to other alignments using the sum-of-pairs metric.
-Remark: May be packaged in local repository
- A local package is mentioned at
- https://www.bioinformatics.uwaterloo.ca/wiki/index.php?Local%20Debian%20Repository
- but the package does not seem to be available publicly.  It might be a good idea to ask
- there before starting packaging.
-Published-Title: LAGAN and Multi-LAGAN: efficient tools for large-scale multiple alignment of genomic DNA
-Published-Authors: Michael Brudno, Chuong Do, Gregory Cooper, Michael F. Kim, Eugene Davydov, Eric D. Green, Arend Sidow, Serafim Batzoglou
-Published-In: Genome Research 13(4):721-31.
-Published-Year: 2003
-Published-URL: http://lagan.stanford.edu/lagan_web/mlagan_gr.pdf
-X-Category: Comparative genomics
 
 Depends: jstreeview
 Homepage: http://www.sanger.ac.uk/Users/lh3/treeview.shtml


