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 <o...@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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/
--
***************************************
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>
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client. To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
http://lists.bx.psu.edu/