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. > > --nate > >> >> Peter >> > ___________________________________________________________ > 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: > > http://lists.bx.psu.edu/ -- Ravi K Madduri The Globus Alliance | Argonne National Laboratory | University of Chicago http://www.mcs.anl.gov/~madduri
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