<div dir="ltr">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.<br></div><br><div class="gmail_quote"><div dir="ltr">On Thu, Oct 25, 2018 at 10:30 AM Park, Gisoo (gp4r) via OOD-users <<a href="mailto:ood-users@lists.osc.edu">ood-users@lists.osc.edu</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
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<p class="MsoNormal">Hello Shawn,<u></u><u></u></p>
<p class="MsoNormal">Do you have update on this? We are also interested in using Galaxy with OOD and wondering if you have any update for it.<u></u><u></u></p>
<p class="MsoNormal">Best,<u></u><u></u></p>
<p class="MsoNormal">Gisoo<u></u><u></u></p>
<p class="MsoNormal">University of Virginia<u></u><u></u></p>
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<p class="MsoNormal"><b><span style="font-size:12.0pt;color:black">From: </span></b><span style="font-size:12.0pt;color:black">OOD-users <<a href="mailto:ood-users-bounces@lists.osc.edu" target="_blank">ood-users-bounces@lists.osc.edu</a>> on behalf of Shawn Doughty <<a href="mailto:shawn.doughty@tufts.edu" target="_blank">shawn.doughty@tufts.edu</a>><br>
<b>Reply-To: </b>User support mailing list for Open OnDemand <<a href="mailto:ood-users@lists.osc.edu" target="_blank">ood-users@lists.osc.edu</a>><br>
<b>Date: </b>Saturday, September 29, 2018 at 1:51 PM<br>
<b>To: </b>User support mailing list for Open OnDemand <<a href="mailto:ood-users@lists.osc.edu" target="_blank">ood-users@lists.osc.edu</a>><br>
<b>Subject: </b>Re: [OOD-users] OnDemand Galaxy<u></u><u></u></span></p>
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<p class="MsoNormal"><u></u> <u></u></p>
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<p class="MsoNormal"><a name="m_-8715467633461028952__MailOriginalBody">Thanks for the suggestions, I'll definitely let everyone know once I get this working.<u></u><u></u></a></p>
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<p class="MsoNormal"><span><u></u> <u></u></span></p>
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<p class="MsoNormal"><span>On Fri, Sep 28, 2018, 12:02 PM Franz, Eric <</span><a href="mailto:efranz@osc.edu" target="_blank"><span>efranz@osc.edu</span><span></span></a><span>>
wrote:<u></u><u></u></span></p>
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<p class="MsoNormal"><span>Shawn,<u></u><u></u></span></p>
<p class="MsoNormal"><span> <u></u><u></u></span></p>
<p class="MsoNormal"><span>We haven’t tried yet, but looks like you are making good progress!<u></u><u></u></span></p>
<p class="MsoNormal"><span> <u></u><u></u></span></p>
<p class="MsoNormal"><span>Have you configured Galaxy to run at the suburi /node/m3n08/8080?<u></u><u></u></span></p>
<p class="MsoNormal"><span> <u></u><u></u></span></p>
<p class="MsoNormal"><span>Note that if you are using /node/ proxy, that means that Galaxy needs to be configured at a suburi that matches that url.
<u></u><u></u></span></p>
<p class="MsoNormal"><span> <u></u><u></u></span></p>
<p class="MsoNormal"><span>According to
</span><a href="https://docs.galaxyproject.org/en/latest/admin/special_topics/nginx.html#basic-configuration" target="_blank"><span>https://docs.galaxyproject.org/en/latest/admin/special_topics/nginx.html#basic-configuration</span><span></span></a><span>
the default Galaxy configuration . These directions for “Serving Galaxy at a sub directory” might help:
</span><a href="https://docs.galaxyproject.org/en/latest/admin/special_topics/nginx.html#serving-galaxy-at-a-sub-directory-such-as-galaxy" target="_blank"><span>https://docs.galaxyproject.org/en/latest/admin/special_topics/nginx.html#serving-galaxy-at-a-sub-directory-such-as-galaxy</span><span></span></a><span>.
<u></u><u></u></span></p>
<p class="MsoNormal"><span> <u></u><u></u></span></p>
<p class="MsoNormal"><span>> 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<u></u><u></u></span></p>
<p class="MsoNormal"><span>> <u></u><u></u></span></p>
<p class="MsoNormal"><span>>[filter:proxy-prefix]<u></u><u></u></span></p>
<p class="MsoNormal"><span>>use = egg:PasteDeploy#prefix<u></u><u></u></span></p>
<p class="MsoNormal"><span>>prefix = /galaxy<u></u><u></u></span></p>
<p class="MsoNormal"><span>> <u></u><u></u></span></p>
<p class="MsoNormal"><span>>[app:main]<u></u><u></u></span></p>
<p class="MsoNormal"><span>>filter-with = proxy-prefix<u></u><u></u></span></p>
<p class="MsoNormal"><span>>cookie_path = /galaxy<u></u><u></u></span></p>
<p class="MsoNormal"><span> <u></u><u></u></span></p>
<p class="MsoNormal"><span>Note in your case prefix would need to be /node/m3n08/8080.<u></u><u></u></span></p>
<p class="MsoNormal"><span> <u></u><u></u></span></p>
<p class="MsoNormal"><span>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.<u></u><u></u></span></p>
<p class="MsoNormal"><span> <u></u><u></u></span></p>
<p class="MsoNormal"><span>Also, if you get this working could you share how you did it?<u></u><u></u></span></p>
<p class="MsoNormal"><span> <u></u><u></u></span></p>
<p class="MsoNormal"><span>Thanks,<u></u><u></u></span></p>
<p class="MsoNormal"><span>Eric<u></u><u></u></span></p>
<p class="MsoNormal"><span> <u></u><u></u></span></p>
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<p class="MsoNormal"><span>---<u></u><u></u></span></p>
<p class="MsoNormal"><span>Eric Franz, Senior Web & Interface App Engineer<u></u><u></u></span></p>
<p class="MsoNormal"><span>Ohio Supercomputer Center<u></u><u></u></span></p>
<p class="MsoNormal"><span>An Ohio Technology Consortium (OH-TECH) Member<u></u><u></u></span></p>
<p class="MsoNormal"><span>1224 Kinnear Road<u></u><u></u></span></p>
<p class="MsoNormal"><span>Columbus, OH 43212<u></u><u></u></span></p>
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<p class="MsoNormal"><span>email:
</span><a href="mailto:efranz@osc.edu" target="_blank"><span>efranz@osc.edu</span><span></span></a><span><u></u><u></u></span></p>
<p class="MsoNormal"><span> <u></u><u></u></span></p>
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<p class="MsoNormal"><span><b><span style="font-size:12.0pt;color:black">From:
</span></b></span><span><span style="font-size:12.0pt;color:black">OOD-users <</span></span><a href="mailto:ood-users-bounces@lists.osc.edu" target="_blank"><span><span style="font-size:12.0pt">ood-users-bounces@lists.osc.edu</span></span><span></span></a><span><span style="font-size:12.0pt;color:black">>
on behalf of Shawn Doughty <</span></span><a href="mailto:shawn.doughty@tufts.edu" target="_blank"><span><span style="font-size:12.0pt">shawn.doughty@tufts.edu</span></span><span></span></a><span><span style="font-size:12.0pt;color:black">><br>
<b>Reply-To: </b>User support mailing list for Open OnDemand <</span></span><a href="mailto:ood-users@lists.osc.edu" target="_blank"><span><span style="font-size:12.0pt">ood-users@lists.osc.edu</span></span><span></span></a><span><span style="font-size:12.0pt;color:black">><br>
<b>Date: </b>Wednesday, September 26, 2018 at 1:59 PM<br>
<b>To: </b>User support mailing list for Open OnDemand <</span></span><a href="mailto:ood-users@lists.osc.edu" target="_blank"><span><span style="font-size:12.0pt">ood-users@lists.osc.edu</span></span><span></span></a><span><span style="font-size:12.0pt;color:black">><br>
<b>Subject: </b>[OOD-users] OnDemand Galaxy</span><u></u><u></u></span></p>
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<p class="MsoNormal"><span> <u></u><u></u></span></p>
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<p class="MsoNormal"><span>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.<u></u><u></u></span></p>
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<p class="MsoNormal"><span> <u></u><u></u></span></p>
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<p class="MsoNormal"><span>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"<u></u><u></u></span></p>
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<p class="MsoNormal"><span> <u></u><u></u></span></p>
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<p class="MsoNormal"><span>view.html.erb is using <form action="/node/<%= host %>/<%= port %>" method="post" target="_blank"><u></u><u></u></span></p>
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<p class="MsoNormal"><span> <u></u><u></u></span></p>
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<p class="MsoNormal"><span>I can get to the port manually from another node via lynx, etc.<br clear="all">
<u></u><u></u></span></p>
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<p class="MsoNormal"><span><br>
-- <u></u><u></u></span></p>
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<p class="MsoNormal"><span><span style="font-size:10.0pt;font-family:Helvetica">Shawn G. Doughty<br>
Manager - Research Computing</span><br>
</span><span><span style="font-size:10.0pt;font-family:Helvetica">Tufts Technology Services (TTS)</span><u></u><u></u></span></p>
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<p class="MsoNormal"><span>Research Technology (RT)<u></u><u></u></span></p>
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<p class="MsoNormal"><span>16 Dearborn Road<br>
Somerville, MA 02144</span><span><span style="font-size:10.0pt;font-family:Helvetica"><br>
617-627-5462<br>
</span></span><a href="https://exchange.tufts.edu/owa/redir.aspx?C=I4ijzFrF9U-qoUscfQAAw3PH17xA188ItQ-l2VPx05symHhOFT2FNSr8FiNXjMnyEtzrTlLLj-Q.&URL=http%3a%2f%2fit.tufts.edu%2f" target="_blank"><span><span style="font-size:10.0pt;font-family:Helvetica">http://it.tufts.edu/</span></span><span></span></a><span><u></u><u></u></span></p>
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</blockquote></div><br clear="all"><br>-- <br><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr">
<span style="font-family:"Segoe UI",Helvetica,Arial,sans-serif;font-size:13.6px">Shawn G. Doughty</span><br style="font-family:"Segoe UI",Helvetica,Arial,sans-serif;font-size:13.6px">
<span style="font-family:"Segoe UI",Helvetica,Arial,sans-serif;font-size:13.6px">Manager - Research Computing</span><br>
<span dir="ltr"><font face="Helvetica"><span style="font-weight:normal;font-variant:normal;text-transform:none"><span style="font-family:"Segoe UI",Helvetica,Arial,sans-serif;font-size:13.6px">Tufts Technology Services (TTS)</span></span></font></span><br>
</div><div dir="ltr"><span><span style="font-family:"Segoe UI",Helvetica,Arial,sans-serif;font-size:13.6px"></span>Research Technology (RT)<br></span></div><div dir="ltr">16 Dearborn Road<br>
Somerville, MA 02144<br style="font-family:"Segoe UI",Helvetica,Arial,sans-serif;font-size:13.6px">
<span style="font-family:"Segoe UI",Helvetica,Arial,sans-serif;font-size:13.6px">617-627-5462<br>
</span><a href="https://exchange.tufts.edu/owa/redir.aspx?C=I4ijzFrF9U-qoUscfQAAw3PH17xA188ItQ-l2VPx05symHhOFT2FNSr8FiNXjMnyEtzrTlLLj-Q.&URL=http%3a%2f%2fit.tufts.edu%2f" style="font-family:"Segoe UI",Helvetica,Arial,sans-serif;font-size:13.6px" target="_blank">http://it.tufts.edu/</a></div></div></div></div></div></div>