[Blends-commit] r2794 - /projects/med/trunk/debian-med/tasks/bio

Fri Apr 29 07:07:01 UTC 2011

Author: tille
Date: Fri Apr 29 07:06:32 2011
New Revision: 2794

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2794
Log:
Abacas and maqview are now official packages

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=2794&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Fri Apr 29 07:06:32 2011
@@ -48,6 +48,8 @@
  maintainer a note if you have any news of this project.
 
 Depends:     boxshade, fastx-toolkit, gff2aplot, muscle, sim4, sibsim4, tabix, wise
+
+Depends:     maqview
 
 Depends: bwa
 Published-Title: Fast and accurate short read alignment with Burrows-Wheeler transform
@@ -3088,6 +3090,10 @@
 
 Depends: qiime
 
+Depends: biomaj
+
+Depends: abacas
+
 Depends: denoiser
 WNPP: 587274
 Homepage:  http://www.microbio.me/denoiser/
@@ -3112,30 +3118,6 @@
  curves.  It provides a GUI for the Debian packaged r-bioc-hilbertvis and is thus
  interesting for giving users some comfort.  Until this software is not yet packaged
  you can follow the hint at the homepage how to use it with R.
-
-Depends: maqview
-Homepage: http://maq.sourceforge.net/maqview.shtml
-WNPP: 604497
-License: GPL2
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/maqview/trunk/
-Responsible: Andreas Tille <tille at debian.org>
-Pkg-Description: graphical read alignment viewer for short gene sequences
- Maqview is graphical read alignment viewer. It is specifically designed
- for the Maq alignment file and allows you to see the mismatches, base
- qualities and mapping qualities. Maqview is nothing fancy as Consed or
- GAP, but just a simple viewer for you to see what happens in a
- particular region.
- .
- In comparison to tgap-maq, the text-based read alignment viewer writen
- by James Bonfield, Maqview is faster and takes up much less memory and
- disk space in indexing. This is possibly because tgap aims to be a
- general-purpose viewer but Maqview fully makes use of the fact that a
- Maq alignment file has already been sorted. Maqview is also efficient in
- viewing and provides a command-line tool to quickly retrieve any region
- in an Maq alignment file.
- .
- Maqview is based on OpenGL. Installing OpenGL on your system is the                                       trade-off of getting a better feel and look. The following screenshots
- show the two viewing modes of Maqview.
 
 Depends: pal2nal
 WNPP: 604701
@@ -3158,8 +3140,6 @@
 Published-Authors: Mikita Suyama, David Torrents, and Peer Bork
 Published-In: Nucleic Acids Res. 34:W609-W612
 Published-Year: 2006
-
-Depends: biomaj
 
 Depends: sra-sdk
 Homepage: http://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?cmd=show&f=software&m=software&s=software
@@ -3304,27 +3284,6 @@
  using Mauve which produces alignment of whole bacterial genomes in
  exactly the format required for analysis with ClonalFrame.
 
-Depends: abacas
-Homepage: http://abacas.sourceforge.net/
-License: GPL
-Language: Perl
-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/
-Pkg-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.
-
 Depends: zodiac
 Homepage: http://www.zeden.org/
 License: GPL


