Thanks Dannon for adding the Phylogenetics category,
I changed the name of this thread, to go in a related by new direction:

I wonder if the Galaxy developers and community have any opinions on what is the best way to organize tools into repositories. We've developed a large number of tools to allow my lab to conduct phylogenetic analyses in Galaxy. Inspired by the mothur package in Galaxy, which is all in one repo, I made the decision to add all our related tools to 1 repo on the tool shed. However, it seems that makes individual tools like raxml difficult to find for other users.  Recently, we started putting these tools on to bitbucket, and organizing them in different categories (alignment, phylogenetics, orthologies, etc), which is a compromise between all-in-one-repo and each-its-own-repo.

The thing is that many of the tools do not stand alone, and really are designed to function with other tools in the package. Any philosophies or opinions are welcome, as I feel like I have not come to a good solution on this...

Todd




On 10/29/2012 1:50 PM, Dannon Baker wrote:
On Oct 29, 2012, at 4:40 PM, Oleksandr Moskalenko <om@hpc.ufl.edu> wrote:


This is an interesting project. I'm glad to see more people working on phylogenetics related wrappers and workflows. I wonder if we could get a "Phylogenetics" category added to the main Galaxy Toolshed, so we could put all the relevant wrappers in there to make them easier to find considering the apparent duplication of efforts.

Good idea, the main toolshed now has a Phylogenetics category.

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