[Blends-commit] r3349 - /projects/med/trunk/debian-med/tasks/bio

Wed May 23 20:14:40 UTC 2012

Author: tille
Date: Wed May 23 20:14:40 2012
New Revision: 3349

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=3349
Log:
Remove some now redundant information which is drawn from UDD

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=3349&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Wed May 23 20:14:40 2012
@@ -196,13 +196,6 @@
 Depends: seq-gen
 
 Depends: mira-assembler
-
-Depends: bagphenotype
-Homepage: http://www.unc.edu/~wvaldar/bagphenotype.html
-License: GPL-3
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/bagphenotype/bagphenotype/trunk/
-Pkg-Description: CLI for the bagphenotype R package
- mapping QTLs in populations descended from known founders
 
 Depends: r-other-valdar-bagphenotype.library
 Homepage: http://www.unc.edu/~wvaldar/bagphenotype.html
@@ -332,33 +325,21 @@
 
 Depends: anfo
 
+Depends: axparafit, axpcoords
+
+Depends: bagphenotype
+
+Depends: beast-mcmc
+Pkg-URL: http://people.debian.org/~tille/packages/beast-mcmc-help-wanted/
+Remark: Name space pollution
+ There is a Debian package beast which is completely unrelated
+ to this project.
+ .
+ The upload of the package is somehow blocked because the last binary
+ Jar which is included inside the source (mtj.jar) is quite hard to
+ package.
+
 X-Mark: The information below needs to be checked whether it can be obtained from Vcs or needs to stay here
-
-Depends: axparafit
-Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
-Responsible: David Paleino <d.paleino at gmail.com>
-License: GPL
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/axparafit/trunk/
-WNPP: 464323
-Pkg-Description: optimized statistical analysis of host-parasite coevolution
- AxParafit is a highly optimized version of Pierre Legendre's Parafit
- program for statistical analysis of host-parasite coevolution.
- AxParafit has been parallelized with MPI (Message Passing Interface)
- for compute clusters and was used to carry out the largest
- co-evolutionary analysis to date for the paper describing the software.
-
-Depends: axpcoords
-Homepage: http://icwww.epfl.ch/~stamatak/AxParafit.html
-Responsible: David Paleino <d.paleino at gmail.com>
-License: GPL
-WNPP: 464323
-Pkg-Description: LAPACK-based implementation of DistPCoA
- AxPcoords is a fast, LAPACK-based implementation of DistPCoA (see
- http://www.bio.umontreal.ca/Casgrain/en/labo/distpcoa.html)
- which is another program by Pierre Legendre, it conducts a principal
- coordinates analysis.
- This program is required for the pipeline that conducts a full host-parasite
- co-phylogenetic analysis in combination with AxParafit.
 
 Depends: copycat
 Homepage: http://www-ab.informatik.uni-tuebingen.de/software/copycat/welcome.html
@@ -1485,40 +1466,6 @@
  bp/s. Additional extensions to tRNAscan-SE detect unusual tRNA
  homologues such as selenocysteine tRNAs, tRNA-derived repetitive
  elements and tRNA pseudogenes.
-
-Depends: beast-mcmc
-Homepage: http://beast.bio.ed.ac.uk/
-License: LGPL
-WNPP: 552101
-Responsible: Andreas Tille <tille at debian.org>
-Pkg-URL: http://people.debian.org/~tille/packages/beast-mcmc-help-wanted/
-Vcs-Svn: svn://svn.debian.org/debian-med/trunk/packages/beast-mcmc/trunk/
-Pkg-Description: Bayesian MCMC analysis of molecular sequences
- BEAST is a cross-platform program for Bayesian MCMC analysis of
- molecular sequences.  It is entirely orientated towards rooted,
- time-measured phylogenies inferred using strict or relaxed molecular
- clock models. It can be used as a method of reconstructing
- phylogenies but is also a framework for testing evolutionary
- hypotheses without conditioning on a single tree topology. BEAST uses
- MCMC to average over tree space, so that each tree is weighted
- proportional to its posterior probability. We include a simple to use
- user-interface program for setting up standard analyses and a suit of
- programs for analysing the results.
- .
- The source is avialable at http://code.google.com/p/beast-mcmc/ .
-Remark: Name space pollution
- There is a Debian package beast which is completely unrelated
- to this project.
- .
- The upload of the package is somehow blocked because the last binary
- Jar which is included inside the source (mtj.jar) is quite hard to
- package.  Any help is welcome.
-Published-Title: BEAST: Bayesian evolutionary analysis by sampling trees
-Published-Authors: A. J. Drummond, A. Rambaut
-Published-In: BMC Evolutionary Biology
-Published-URL: http://www.biomedcentral.com/1471-2148/7/214/abstract
-Published-DOI: 10.1186/1471-2148-7-214
-Published-PubMed: 17996036
 
 Depends: artemis
 Homepage: http://www.sanger.ac.uk/Software/Artemis/


