[OOD-users] OnDemand Galaxy

[Shawn Doughty]

Not yet, I've been dealing with a # system emergencies. So far galaxy
starts up, outputs a web page but it doesn't render in the browser. I
suspect that there needs to be a real web server (apache, nginx) configured
in front of galaxy just as if it were in a more traditional web front-end
setup. Was hoping to avoid this and just make it work with the built in
default python web server.  if anyone figure sit out let me know. Will
continue working on the issue as soon as I can.

On Thu, Oct 25, 2018 at 10:30 AM Park, Gisoo (gp4r) via OOD-users <
ood-users at lists.osc.edu> wrote:

> 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> 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
>
>
>
> *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: *Wednesday, September 26, 2018 at 1:59 PM
> *To: *User support mailing list for Open OnDemand <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>
>
>

-- 
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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