[Blends-commit] r3396 - /projects/med/trunk/debian-med/tasks/bio

[tille at users.alioth.debian.org]

Author: tille
Date: Wed Jun  6 14:34:15 2012
New Revision: 3396

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3396
Log:
Removed redundant information from qtlreaper and vmd

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=3396&op=diff
==============================================================================
--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Wed Jun  6 14:34:15 2012
@@ -406,6 +406,8 @@
 
 Depends: proalign
 
+Depends: python-reaper
+
 Depends: r-other-valdar-bagphenotype.library
 
 Depends: ray-denovoassembler
@@ -432,6 +434,8 @@
 X-Depends: treevolve
 X-Comment: Homepage of software vanished, packaging in SVN is obviosely stalled
  Feel free to delete the 'X-' in front if you intend to do something on this package
+
+Depends: vmd
 
 Depends: wgs-assembler
 Note: Genome assembly and large-scale genome alignment (http://www.cbcb.umd.edu/software/)
@@ -2678,25 +2682,6 @@
  techniques. It can be used through a nice and intuitive user interface
  or, for more advanced users, as a module for Python programming language.
 
-Depends: python-reaper
-Homepage: http://qtlreaper.sf.net
-License: GPL-2+
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/qtlreaper/trunk/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/qtlreaper/trunk/
-Pkg-Description: QTL analysis for expression data
- QTL Reaper is software, written in C and compiled as a Python module, for
- rapidly scanning microarray expression data for QTLs. It is essentially
- the batch-oriented version of WebQTL. It requires, as input, expression
- data from members of a set of recombinant inbred lines and genotype
- information for the same lines. It searches for an association between
- each expression trait and all genotypes and evaluates that association
- by a permutation test. For the permutation test, it performs only as
- many permutations as are necessary to define the empirical P-value to a
- reasonable precision. It also performs bootstrap resampling to estimate
- the confidence region for the location of a putative QTL.
- .
- The reaper module is used underneath the http://genenetwork.org site.
-
 Depends: sequenceconverter.app
 Homepage: http://bioinformatics.org/biococoa/
 License: GPL
@@ -2724,25 +2709,6 @@
 
 Depends: ugene
 
-Depends: vmd
-License: non-free
-Homepage: http://www.ks.uiuc.edu/Research/vmd/
-Vcs-Browser: http://svn.debian.org/wsvn/debichem/wnpp/vmd/
-Vcs-Svn: svn://svn.debian.org/svn/debichem/wnpp/vmd/
-Responsible: Michael Banck <mbanck at debian.org>, Steffen Moeller <moeller at debian.org>
-Pkg-Description: presentation of traces of molecular dynamics runs
- VMD stands for Visual Molecular Dynamics. While text books
- and even structure databases because of technical problems only
- present static pictures of proteins or DNA, for the understanding
- of the properties of those molecules their vibration or their
- movement in general is important.
- .
- The movements itself are calculated by molecular dynamics programs,
- such as NAMD (by the same group), Rosetta, BALLView or GROMACS. The
- latter two are already in the distribution. VMD has a series of
- nice features, from displaying through animation to analysing.
- It can be scripted, clustered, and runs on all common OS.
-
 Depends: vegan
 WNPP: 659863
 Homepage: http://vegan.r-forge.r-project.org/