Keith, please see the comments inline.
thanks
M.

On Fri, Sep 11, 2015 at 4:54 PM Suderman Keith <suder...@cs.vassar.edu>
wrote:

> Hi Martin,
>
> On Sep 11, 2015, at 12:44 PM, Martin Čech <mar...@bx.psu.edu> wrote:
>
> 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>.
>

That is correct for packages and suites but incorrect for tools. Sorry for
the confusion.


>
> 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.
>

In this case the naming kinda makes sense to me (lapps_stanford_2_0_0 and
lapps_stanford_2_1_0 that is). However could the remote Standford API
version be a parameter of the tool instead? i.e. you would have only
'lapps_stanford' and select the version you want to use from a dropdown and
the tool form would adjust (this is technically possible and used) and
after execution called the right underlying script?


>
> 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
>
> On Fri, Aug 7, 2015 at 2:57 PM Martin Čech <mar...@bx.psu.edu> wrote:
>
>> No sub-categories yet; we plan on tackling the browsing issue by having
>> good search. :)
>>
>> M.
>>
>> On Fri, Aug 7, 2015 at 2:43 PM Keith Suderman <suder...@cs.vassar.edu>
>> wrote:
>>
>>> 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
>>>
>>> On Aug 7, 2015, at 12:25 PM, Martin Čech <mar...@bx.psu.edu> wrote:
>>>
>>> Dear Keith,
>>>
>>> I have created 'NLP' category at https://testtoolshed.g2.bx.psu.edu for
>>> you to test out the Tool Shed environment.
>>>
>>> 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
>>>
>>>
>>> On Fri, Aug 7, 2015 at 12:56 PM Björn Grüning <bjoern.gruen...@gmail.com>
>>> wrote:
>>>
>>>> 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
>>>> >
>>>> >
>>>> > ___________________________________________________________ Please
>>>> > keep all replies on the list by using "reply all" in your mail
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>>>> >
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>>>> >
>>>>
>>>
>>> ------------------------------
>>> Research Associate
>>> Department of Computer Science
>>> Vassar College
>>> Poughkeepsie, NY
>>>
>>>
>>>
>
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