On Fri, Jul 18, 2014 at 4:21 PM, Eric Rasche <rasche.e...@yandex.ru> wrote:
> On 07/18/2014 09:49 AM, John Chilton wrote:
>> My understanding of the code is that tool shed dependencies (or local
>> dependencies) will not be available to tool shed datatypes (for
>> sniffing for instance). Sorry.
>
> I figured as much, not very surprising at all. Dependencies
> notwithstanding, the idea has some modicum of merit. There are plenty of
> people who have already written great parsers that throw up errors, why
> should datatypes re-write them?

Exactly - Trello request for the toolshed to handle both Python and
binary dependencies for datatypes?

(e.g. samtools is a binary dependency of the SAM/BAM datatypes,
used for conversion and indexing)

>> If you want to hack up your local instance to resolve dependencies
>> during the sniffing process that may be possible - my guess is you
>> could add requirement tags to tools/data_source/upload.xml and the
>> __SET_METADATA__ tool definition embedded in
>> lib/galaxy/datatypes/registry.py - though I have not tried this.
>
> Well heck, at that point I'd just use the fact that I know I'm in
> lib/galaxy/datatypes to locate the BioPython dependency that was
> installed through greps, globs, and finds. Though I'll hold off on that
> for a "better" solution.

I'd manually install the Python dependencies as part of the Python
used to run Galaxy itself?

Peter
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