(apologies in advance, limiting my response to the two questions below)

On Jun 1, 2011, at 11:54 AM, Peter Cock wrote:

> On Wed, Jun 1, 2011 at 5:25 PM, Nate Coraor <n...@bx.psu.edu> wrote:
>> Peter Cock wrote:
>>> 
>>> Well, yes and no - as long as there are competing versions of a Galaxy tool
>>> (e.g. from an original author and a fork by a second author), and they use
>>> the same ID in their XML, you have a clash. This will have to be considered
>>> in the (automated) install interface. i.e. In general, when installing or
>>> updating any tool, there may be existing versions of some components
>>> already present. In fact two completely unrelated tools could even have
>>> the same XML ID by accident.
>> 
>> I agree there could be a problem with tool ID uniqueness.  We've talked
>> about suggesting that people namespace their tool IDs to prevent this,
>> but nothing formal has materialized at this point.
> 
> That sounds sensible, and the sooner the better.

Agreed.  I think simple namespace prefixes (maybe hg account?) is the easiest 
option.

>>> I'm not immediately sold on this plan. To me one of the big plus points
>>> of having a single "Official" Tool Shed looked after by the Galaxy team
>>> is the convenience factor (a one stop shop), which requires critical mass,
>>> plus whatever QA happens as part of the current approval process. I
>>> would regard it as a step backwards if in order to hunt for a wrapper for
>>> a given tool, I had to resort to Google in order to find all the individual
>>> Galaxy Tool Sheds.
>> 
>> It'll be possible for people to run their own Tool Sheds if they'd like,
>> for whatever purpose - and this may be necessary for sharing extremely
>> large data which we can't possibly host at the main Shed, but there
>> should be an aggregator somewhere which lists all of the available
>> public Sheds and makes it easy to add them as new sources to your Galaxy
>> install.  Like a slightly more organized Debian APT system.
> 
> If there is an official "meta tool shed" aggregator, that would address
> my main concern about fragmenting things.

Not sure how feasible this is, but could you use hg subrepositories for this 
purpose?  For instance, have a 'blessed' set of galaxy tool sheds (as subrepos) 
listed in a main tool shed repository.  One of the nice advantages of this is 
it could allow one to use git or svn, though I think sticking with hg-only 
repos is the simplest option for now.

chris

PS - wonderful conference, sorry that Peter couldn't make it!


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