[galaxy-dev] The new hg based Galaxy Tool Shed

[Peter Cock]

On Wednesday, June 1, 2011, Chris Fields <cjfields at illinois.edu> wrote:
> (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 <nate at 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.

That sounds good - although I'd suggest the group's name might be a
valid alternative - then an underscore or hyphen, and the tool specific
ID which would typically be based on the name of the tool being wrapped.

If it were up to me I'd go further and recommend a restricted set of
characters (e.g. Alphanumeric and one of hyphen and underscore),
with the additional recommendation that the tool's XML filename
follows suit. e.g. signalp.xml with ID peterjc-signalp

Obviously we'd have to have a "grandfather clause" exemption for
all tools to date because changing their ID would break saved
workflows.

As an aside, I regret including the word "wrapper" in the NCBI
BLAST+ wrappers since most Galaxy tools are just wrappers
around existing tools, but it's done now.

Peter