Hi Keith,
how is the NLP category working for you? Do you want it on Main Tool Shed?
The NLP category is working great. I am still in the early testing phase and likely won't need anything in Main for some time yet, but Steve Cassidy might have a different opinion.
Also I have noticed you are putting the version of your tools in the repository names. I would like to discourage that as it will create confusion once you update your tool (as you will be unable to update the repo name). The XML wrappers have they own version tracking tag for these purposes. You can learn about this and more in the Tooldev Best Practices document:
http://galaxy-iuc-standards.readthedocs.org/en/latest/
I was under the impression (
http://gregvonkuster.org/galaxy-tool-shed-revisiting-best-practices-populating-repository/) that the best practice for package names was package_<name>_<version> and for tools it was <name>_<version>.
There is also some friction (for lack of a better term) between versioning our web services and versioning the Galaxy wrappers that call our web services. For example, I might have multiple versions of the Galaxy wrappers for our stanford_2.0.0 services and multiple versions of the Galaxy wrappers for our stanford_2.1.0 services. The 2.0.0 services are not going away just because the 2.1.0 services are available, so I think the stanford_2.0.0 and stanford_2.1.0 Galaxy wrappers have to be separate repositories.
Having said that, I am planning to remove all my current repositories and repopulate as I try to automate things on my end so suggestions for naming strategies are always welcome.
"There are only two hard problems in computer science, cache invalidation and naming things"
- author unknown
Thank you for using Galaxy.
Thank you (all) for making Galaxy! ;-)
Cheers,
Keith
Martin
No sub-categories yet; we plan on tackling the browsing issue by having good search. :)
Awesome!
One concern we have is lumping all NLP tools into a single category; are sub-categories (and sub-sub-categories) possible? However, we can start with this and see what we need later.
Cheers,
Keith
Dear Keith,
Unless your tools are proprietary I strongly recommend using the Main Tool Shed at
https://toolshed.g2.bx.psu.edu for their publishing and distribution. Let me know when you are ready with the tools and I will create the category for you in there.
We happily welcome every tool contribution to Galaxy! Thank you for it.
Martin, Galaxy Team
Hi Keith,
the Galaxy team can add new categories to the Tool Shed very easily and
such a mail is exactly the way to go. As soon as the Galaxy teams has
added the category you can use tools like planemo to upload all your
tools at once.
https://github.com/galaxyproject/planemo
Looking forward to see NLP tools in Galaxy and the Main TS! Awesome!
Bjoern
> Dear Galaxy Team,
>
> A colleague would like to upload some NLP (Natural Language
> Processing) tools to the Galaxy Test/Main tools sheds, but we are
> unclear what "categories" to use for the tools. I see that the
> Main/Test tools sheds have a category for "Text Manipulation", but
> that does not seem appropriate for NLP tools. Is it possible to have
> new categories added to the tool shed(s)? If so, what is the
> process?
>
> I am just starting to investigate setting up our own local tool shed
> and I am coming across mentions of repository capsules and exporting
> tool sheds. Would it be preferable to install the NLP tools to a
> local tool shed and then export a repository/capsule to be imported
> to the Test/Main tools sheds? What happens if our tool shed uses a
> disjoint set of categories than Test/Main?
>
> Cheers, Keith
>
> ------------------------------ Research Associate Department of
> Computer Science Vassar College Poughkeepsie, NY
>
>
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------------------------------
Research Associate
Department of Computer Science
Vassar College
Poughkeepsie, NY