[OOD-users] Galaxy

Fri Apr 27 15:52:18 EDT 2018

We had some discussions about this, ranging from adding a punch out to our existing Galaxy server, to questions about the value of per-user Galaxy when we already have a lot of users. We count SUs, so there is also the philosophical question about whether sitting thinking in front of the Galaxy interface (submitted as a batch job) should burn SUs (seems perfectly OK once you make up your mind and submit a job to do something.) There is also the network part about getting through the back-end network gracefully for modules that need Internet access.

It would be OK for us just to add an item to some OOD menu to redirect to the existing service. Handling authentication to Galaxy using credentials that may be available in a user's OOD context would be cool if possible, but the convenience of having OOD as a focal point for all portal-like services may be enough of a reason to just add a link as a menu item for now.

Rick

——
Donald F. (Rick) McMullen, Ph.D.
Associate Director
High Performance Research Computing
Division of Research

222 Jones Street, Rm. 107
3361 TAMU
College Station, TX 77843-3361

Tel. +1 979.458.8414
mcmullen at tamu.edu
http://hprc.tamu.edu

> On Apr 27, 2018, at 10:39 AM, Franz, Eric <efranz at osc.edu> wrote:
> 
> Shawn,
>  
> I’ve started investigating options for supporting Galaxy at OSC, and it is our preference is to have it integrated into OnDemand.
>  
> Some thoughts include:
>  
> Lots of users are interested in sharing histories, datasets, workflows, etc. and so a shared database for these users would be preferred. SQLite3 over NFS is not ideal for this, and other options require some setup up front for each Galaxy user. There are many other questions regarding using Galaxy in the per-user model.
> It might be possible to have multiple Galaxy instances use the same database (i.e. per user Galaxy), but it is possible that Galaxy doesn’t officially support “horizontal scaling” yet.
>  
> Are you (or anyone else) interested in any level of involvement with this effort?
>  
> Thanks,
> Eric
>  
> ---
> Eric Franz, Senior Web & Interface App Engineer
> Ohio Supercomputer Center
> An Ohio Technology Consortium (OH-TECH) Member
> 1224 Kinnear Road
> Columbus, OH 43212
> email: efranz at osc.edu <mailto:efranz at osc.edu>
> From: OOD-users <ood-users-bounces at lists.osc.edu> on behalf of Shawn Doughty <shawn.doughty at tufts.edu>
> Reply-To: User support mailing list for Open OnDemand <ood-users at lists.osc.edu>
> Date: Monday, April 23, 2018 at 11:44 PM
> To: User support mailing list for Open OnDemand <ood-users at lists.osc.edu>
> Subject: [OOD-users] Galaxy
>  
> What are other sites doing in regard to integrating things like Galaxy into OnDemand? I'm taking a very basic approach which just creates a menu item that does a redirect to the galaxy site. Users login, save their password and it seems integrated. <>
> That being said, I might want to do something more sophisticated so users don't get redirected or otherwise see the site so is anyone sharing authentication between OOD, Galaxy or doing some kind of proxy?
> 
> It would be interesting perhaps to simply bring up individual instances of Galaxy just like any other "web app" such as r server or jupyter notebook.
> 
> Thoughts?
> 
> 
> -- 
> Shawn G. Doughty
> Senior Research Technology Specialist, Research Technology
> Tufts Technology Services (TTS)
> 16 Dearborn Road
> Somerville, MA 02144
> 617-627-5462
> http://it.tufts.edu/ <https://urldefense.proofpoint.com/v2/url?u=https-3A__exchange.tufts.edu_owa_redir.aspx-3FC-3DI4ijzFrF9U-2DqoUscfQAAw3PH17xA188ItQ-2Dl2VPx05symHhOFT2FNSr8FiNXjMnyEtzrTlLLj-2DQ.-26URL-3Dhttp-253a-252f-252fit.tufts.edu-252f&d=DwMGaQ&c=ODFT-G5SujMiGrKuoJJjVg&r=1foyGz7TARVR85rd767e9M3OCUsOwg1S5Nrm5z5Ibn4&m=sVfKl0zBtwwNDQnUYugqnZqKuV1NotySbH2uQEH5tzs&s=aWICQAoDpObeAD_TyjvtQLO8Y2hdkXxE1vU-qNO99Cs&e=>_______________________________________________
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