[galaxy-dev] The new hg based Galaxy Tool Shed
madduri at mcs.anl.gov
Wed Jun 15 22:00:37 EDT 2011
I apologize for jumping on to this thread a bit late. I read below that there is a plan to pull tools into a galaxy installation automagically. I wonder if you plan on providing some kind of API to query the tool registry and discover the tools and install them into an existing galaxy installation.
PS: The link : How to upload, download and install tools under Help seems to be broken.
On Jun 1, 2011, at 3:00 PM, Nate Coraor wrote:
> Peter Cock wrote:
>>> Well, use of the dependency system isn't required, so just setting
>>> things up on the $PATH is always a possibility. I was going to suggest
>>> that your patch could be applied if it was conditional on the local
>>> runner and checked after any <requirement type="package">
>>> dependencies were setup, ...
>> Is that a request for me to update the patch? I've not delved into the
>> job runner code before, so it might take me a bit longer that it would
>> take you. Hint hint ;) I'd help with testing though.
> It's not a completely trivial thing, which is why I didn't do it at the
> time. It's probably something that should be added to the DRM wrapper
> script so that a nice error message can be supplied. I can't think of a
> way to check at tool load that wouldn't be painfully slow.
>>> ... but there's still the problem of people running jobs through
>>> the local runner which are actually sent to the cluster without Galaxy's
>>> knowledge. Perhaps this is something we shouldn't worry too much about,
>>> but I know there are people doing it.
>> You mean if Galaxy blindly calls a tool or script, and that script
>> then submits the job to the cluster? I'd say checking the cluster
>> dependencies there was the tool author's responsibility.
> Yeah, that's the idea. Unfortunately, if the binary isn't installed on
> the Galaxy server (which is irrelevant), the tool won't load, which is
> certainly not what we want.
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Ravi K Madduri
The Globus Alliance | Argonne National Laboratory | University of Chicago
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