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

Brilliant, thanks! I had seen the FAQ, but didn't know about configfiles. Much appreciated! 

Ann


-----Original Message-----
From: james@taylorlab.org [mailto:james@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.Gomez@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.gomez@agr.gc.ca Telephone | 
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