On Fri, Jul 18, 2014 at 4:21 PM, Eric Rasche email@example.com 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?