Hi guys,

Noticed that this thread had no further replies. I was wondering if this is going to be in the road map for galaxy next releases. Would be very helpful for sniffing and parsing complex datasets such as medical images.


On Jul 18, 2014 12:42 PM, "Peter Cock" <p.j.a.cock@googlemail.com> wrote:
On Fri, Jul 18, 2014 at 4:21 PM, Eric Rasche <rasche.eric@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?

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:

To search Galaxy mailing lists use the unified search at: