[Blends-commit] r2749 - /projects/med/trunk/debian-med/tasks/bio

Sun Apr 10 19:51:29 UTC 2011

Author: tille
Date: Sun Apr 10 19:51:28 2011
New Revision: 2749

URL: http://svn.debian.org/wsvn/blends/?sc=1&rev=2749
Log:
Fix Homepage field of arachne; mrbayes, pdb2pqr 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=2749&op=diff
==============================================================================

--- projects/med/trunk/debian-med/tasks/bio (original)
+++ projects/med/trunk/debian-med/tasks/bio Sun Apr 10 19:51:28 2011
@@ -317,7 +317,6 @@
 Published-Year: 2009
 Published-URL: http://www.ncbi.nlm.nih.gov/pubmed/19399780
 
-
 Depends: mustang
 Published-Authors: A. S. Konagurthu, J. C. Whisstock, P. J. Stuckey, A. M. Lesk
 Published-Title: MUSTANG: A multiple structural alignment algorithm
@@ -396,6 +395,10 @@
 Depends: paml
 
 Depends: ensembl
+
+Depends: mrbayes
+
+Suggests: pdb2pqr
 
 Depends: r-other-genabel
 Homepage: http://mga.bionet.nsc.ru/nlru/GenABEL/
@@ -2561,30 +2564,6 @@
  surfaces for all populations and all loci.
 Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
 
-Depends: mrbayes
-Homepage: http://mrbayes.csit.fsu.edu/
-License: GPL
-Vcs-Browser: http://svn.debian.org/wsvn/debian-med/trunk/packages/mrbayes/trunk/?rev=0&sc=0
-Vcs-Svn: svn://svn.debian.org/svn/debian-med/trunk/packages/mrbayes/trunk/
-Responsible: BioLinux - Bela Tiwari <btiwari at ceh.ac.uk>
-Pkg-URL: http://nebc.nox.ac.uk/bio-linux/dists/unstable/bio-linux/binary-i386/
-Pkg-Description: Bayesian estimation of phylogeny
- MrBayes is a program for the Bayesian estimation of
- phylogeny. Bayesian inference of phylogeny is based upon a quantity
- called the posterior probability distribution of trees, which is the
- probability of a tree conditioned on the observations. The
- conditioning is accomplished using Bayes's theorem. The posterior
- probability distribution of trees is impossible to calculate
- analytically; instead, MrBayes uses a simulation technique called
- Markov chain Monte Carlo (or MCMC) to approximate the posterior
- probabilities of trees.
- .
- The program takes as input a character matrix in a NEXUS file
- format. The output is several files with the parameters that were
- sampled by the MCMC algorithm. MrBayes can summarize the information
- in these files for the user. The program features include:
-Remark: This package ships with BioLinux http://envgen.nox.ac.uk/biolinux.html
-
 Depends: msatfinder
 Homepage: http://www.genomics.ceh.ac.uk/msatfinder/
 License: GPL
@@ -2999,25 +2978,6 @@
  of biological entities and the specification of is-a (specialisation)
  and part-of relations. Amongst the databases cureated by this tool
  is the GeneOntology.
-
-Suggests: pdb2pqr
-Homepage: http://pdb2pqr.sourceforge.net/
-License: GPL
-WNPP: 416269
-Language: Python, C
-Responsible: Manuel Prinz <debian at pinguinkiste.de>
-Pkg-Description: Converts Protein Data Bank (PDB) files to PQR
- "PDB2PQR is a Python software package that automates many of the
- common tasks of preparing structures for continuum electrostatics
- calculations. This includes adding a limited number of missing
- heavy atoms to biomolecular structures, optimizing the protein
- for favorable hydrogen bonding, determining side-chain pKas, and
- assigning charge and radius parameters from a variety of force
- fields, ultimately yielding a final PQR file."
- .
- PDB2PQR is a tool often used in conjunction with APBS, which is in
- Debian already. I have had good contact with both upstream authors
- in the past.
 
 Depends: lagan
 Homepage: http://lagan.stanford.edu/lagan_web/index.shtml
@@ -3755,7 +3715,7 @@
 Published-doi: 10.1089/cmb.2009.0238
 
 Depends: arachne
-Homepage http://www.broadinstitute.org/crd/wiki/index.php/Arachne
+Homepage: http://www.broadinstitute.org/crd/wiki/index.php/Arachne
 License: free
 Pkg-Description: toolkit for Whole Genome Shotgun Assembly
  Arachne is a toolkit developed for Whole Genome Shotgun Assembly.


