Hi Alex, Todd;  thanks for the info and links! The Garli tool looks a lot more 
sophisticated than what I have so far, so I'm sure it will be helpful to look 
at. 

Ann


-----Original Message-----
From: Oleksandr Moskalenko [mailto:o...@hpc.ufl.edu] 
Sent: Monday, October 29, 2012 4:26 PM
To: Gomez, Ann
Cc: galaxy-dev@lists.bx.psu.edu List
Subject: Re: [galaxy-dev] MrBayes wrapper - set parameters through Galaxy?

Hi Ann,

Configfiles is the way to go. I have writtent the BEAST (and TreeAnnotator), 
Garli, and RAxML wrappers that are all available in the Galaxy ToolShed. BEAST 
uses an input xml file that it can parse to execute the analysis. Garli can 
take a config file that's generated by the Galaxy from the options a user 
selects in the interface. RAxML is a more traditional command-line application 
albeit with very convoluted combinations of inputs and outputs that change on 
every release, which is why my wrapper only supports RAxML 7.3.2. Galaxy 
provides a lot of choices for handling the applications inputs. MrBayes in this 
regard is most similar to Garli, so you can take a look at that wrapper. You 
can take the options from the Galaxy mrbayes interface and write them to a 
config file that can be fed to MrBayes as a separate NEXUS file just as the 
Chapter 5 "How do I run MrBayes in batch mode?" of the MrBayes manual describes.

Regards,

Alex


On Oct 29, 2012, at 2:03 PM, James Taylor <ja...@jamestaylor.org> wrote:

> 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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