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: 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_ba...
-- 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
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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>