[OOD-users] OnDemand Galaxy

[Park, Gisoo (gp4r)]

Hello Shawn,
Do you have update on this? We are also interested in using Galaxy with OOD and wondering if you have any update for it.
Best,
Gisoo
University of Virginia
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: Saturday, September 29, 2018 at 1:51 PM
To: User support mailing list for Open OnDemand <ood-users at lists.osc.edu>
Subject: Re: [OOD-users] OnDemand Galaxy

Thanks for the suggestions, I'll definitely let everyone know once I get this working.

On Fri, Sep 28, 2018, 12:02 PM Franz, Eric <efranz at osc.edu<mailto:efranz at osc.edu>> wrote:
Shawn,

We haven’t tried yet, but looks like you are making good progress!

Have you configured Galaxy to run at the suburi /node/m3n08/8080?

Note that if you are using /node/ proxy, that means that Galaxy needs to be configured at a suburi that matches that url.

According to https://docs.galaxyproject.org/en/latest/admin/special_topics/nginx.html#basic-configuration the default Galaxy configuration . These directions for “Serving Galaxy at a sub directory” might help: https://docs.galaxyproject.org/en/latest/admin/special_topics/nginx.html#serving-galaxy-at-a-sub-directory-such-as-galaxy.

> The Galaxy application needs to be aware that it is running with a prefix (for generating URLs in dynamic pages). This is accomplished by configuring a Paste proxy-prefix filter in the [app:main] section of config/galaxy.ini and restarting Galaxy
>
>[filter:proxy-prefix]
>use = egg:PasteDeploy#prefix
>prefix = /galaxy
>
>[app:main]
>filter-with = proxy-prefix
>cookie_path = /galaxy

Note in your case prefix would need to be /node/m3n08/8080.

Also, OnDemand supports another proxy called /rnode/ which is for servers that use 100% relative URLs, such as noVNC. In that case, there is no need to tell the server what the sub uri/base uri/prefix is since it won’t be using that to build internal hyperlinks.

Also, if you get this working could you share how you did it?

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<mailto:ood-users-bounces at lists.osc.edu>> on behalf of Shawn Doughty <shawn.doughty at tufts.edu<mailto:shawn.doughty at tufts.edu>>
Reply-To: User support mailing list for Open OnDemand <ood-users at lists.osc.edu<mailto:ood-users at lists.osc.edu>>
Date: Wednesday, September 26, 2018 at 1:59 PM
To: User support mailing list for Open OnDemand <ood-users at lists.osc.edu<mailto:ood-users at lists.osc.edu>>
Subject: [OOD-users] OnDemand Galaxy

Has anyone made individual instances of galaxy work in OnDemand? We are doing that in order to provide dev/test instances for team members without having to setup an entire virtual.

I cloned the jupyter, removed all the extra "stuff", hardcoded the port to 8080 and it is almost working. Galaxy starts up, I get a link but clicking returns a "The resource could not be found. No route for /node/m3n08/8080"

view.html.erb is using <form action="/node/<%= host %>/<%= port %>" method="post" target="_blank">

I can get to the port manually from another node via lynx, etc.

--
Shawn G. Doughty
Manager - Research Computing
Tufts Technology Services (TTS)
Research Technology (RT)
16 Dearborn Road
Somerville, MA 02144
617-627-5462
http://it.tufts.edu/<https://exchange.tufts.edu/owa/redir.aspx?C=I4ijzFrF9U-qoUscfQAAw3PH17xA188ItQ-l2VPx05symHhOFT2FNSr8FiNXjMnyEtzrTlLLj-Q.&URL=http%3a%2f%2fit.tufts.edu%2f>
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