(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 

>>> 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.


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

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:


Reply via email to