Ann,
Also to your request "I'd appreciate any input about MrBayes or a similar kind of tool."


We are developing a suite of tools for phylogenetics in Galaxy. We are calling the tool suite Osiris.

We are currently adding the full tool suite to Bit Bucket:
https://bitbucket.org/repo/all?name=osiris_phylogenetics

and many tools are on the tool shed under a repository called ucsb_phylogenetics.

We are describing some of the tools here:

http://osiris-phylogenetics.blogspot.com/



We are in rather active development right now, but the RAxML tools have been 
used rather extensively, and allow some interactive choices (model choice, 
bootstrap reps, DNA v Protein, etc).  We also have a tool for BEAST (very 
simple, just passes the formatted xml file to run the program through Galaxy).  
Another phylogenetic tree estimation tool on the tool shed (not ours) exists 
for GARLI.

We plan to develop a tool for MrBayes, as well, but perhaps we will not have to 
anymore!


Best wishes,

Todd Oakley


On 10/29/2012 11:43 AM, Gomez, Ann wrote:
Brilliant, thanks! I had seen the FAQ, but didn't know about configfiles. Much 
appreciated!

Ann


-----Original Message-----
From: ja...@taylorlab.org [mailto:ja...@taylorlab.org] On Behalf Of James Taylor
Sent: Monday, October 29, 2012 2:03 PM
To: Gomez, Ann
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy?

Ann,

I think you may be able to do this by generating another nexus file using 
"configfiles" in the Galaxy tool config which just contains a command block, 
similar to the example here:

   
http://mrbayes.sourceforge.net/wiki/index.php/FAQ#How_do_I_run_MrBayes_in_batch_mode.3F

-- jt


On Mon, Oct 29, 2012 at 1:24 PM, Gomez, Ann <ann.go...@agr.gc.ca> wrote:
Hello all,



I've written a MrBayes wrapper that accepts a Nexus file (presumably
containing a data block and a command block). In order to make it a
bit easier for new users, I was hoping to be able to  let users
specify some parameters, such as their model, in Galaxy, as opposed to
including it in the command block of the Nexus file. Am I correct in
thinking this is not possible since MrBayes does not have a way to invoke 
commands in-line?



To clarify for non-MrBayes people, my limited understanding is that
you either invoke  the interpreter with "$ mb" and then enter your
commands, or directly execute a Nexus file (containing the data and
commands) with " $ mb <nexusfilename>".



Please correct me if I'm missing something or thinking about this
completely wrong. I'd appreciate any input about MrBayes or a similar kind of 
tool.



Cheers,

Ann



Ann Gomez

Agriculture and Agri-Food Canada | Agriculture et Agroalimentaire
Canada

KW Neatby Bldg | éd. KW Neatby
960 Carling Ave| 960, avenue Carling
Ottawa, ON | Ottawa (ON) K1A 0C6
E-mail Address / Adresse courriel: ann.go...@agr.gc.ca Telephone |
Téléphone 613-759-6805 Facsimile | Télécopieur 613-759-1701 Government
of Canada | Gouvernement du Canada




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--

***************************************
Todd Oakley, Professor
Ecology Evolution and Marine Biology
University of California, Santa Barbara
Santa Barbara, CA 93106 USA
***************************************

Lab Website <http://labs.eemb.ucsb.edu/oakley/todd/>
Twitter: @UCSB_OakleyLab

*Recent Papers: *

 * Pancrustacean Phylotranscriptomics
   MBE Paper
   
<http://mbe.oxfordjournals.org/content/early/2012/09/12/molbev.mss216.abstract>

 * Convergent Evolution in Cephalopoda
   BMC Ev Biol <http://www.biomedcentral.com/1471-2148/12/129/abstract>
 * Cnidocyte discharge regulated by opsin and light
   BMC Biology Paper <http://tinyurl.com/7dajl2q> Scientific American
   Write-up
   
<http://blogs.scientificamerican.com/science-sushi/2012/03/05/hydra-watch-what-they-eat/>

 * Sponge Larvae Could be Guided by Cryptochrome
   J Exp Biol. Paper <http://jeb.biologists.org/content/215/8/ii> |
   Nature News
   <http://www.nature.com/nature/journal/v484/n7393/full/484145d.html>

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