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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hello Shawn,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Do you have update on this? We are also interested in using Galaxy with OOD and wondering if you have any update for it.<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Best,<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Gisoo<o:p></o:p></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">University of Virginia<o:p></o:p></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 <ood-users-bounces@lists.osc.edu> on behalf of Shawn Doughty <shawn.doughty@tufts.edu><br>
<b>Reply-To: </b>User support mailing list for Open OnDemand <ood-users@lists.osc.edu><br>
<b>Date: </b>Saturday, September 29, 2018 at 1:51 PM<br>
<b>To: </b>User support mailing list for Open OnDemand <ood-users@lists.osc.edu><br>
<b>Subject: </b>Re: [OOD-users] OnDemand Galaxy<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a name="_MailOriginalBody">Thanks for the suggestions, I'll definitely let everyone know once I get this working.<o:p></o:p></a></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span style="mso-bookmark:_MailOriginalBody">On Fri, Sep 28, 2018, 12:02 PM Franz, Eric <</span><a href="mailto:efranz@osc.edu"><span style="mso-bookmark:_MailOriginalBody">efranz@osc.edu</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody">>
wrote:<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">Shawn,<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">We haven’t tried yet, but looks like you are making good progress!<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">Have you configured Galaxy to run at the suburi /node/m3n08/8080?<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">Note that if you are using /node/ proxy, that means that Galaxy needs to be configured at a suburi that matches that url.
<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">According to
</span><a href="https://docs.galaxyproject.org/en/latest/admin/special_topics/nginx.html#basic-configuration" target="_blank"><span style="mso-bookmark:_MailOriginalBody">https://docs.galaxyproject.org/en/latest/admin/special_topics/nginx.html#basic-configuration</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody">
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 style="mso-bookmark:_MailOriginalBody">https://docs.galaxyproject.org/en/latest/admin/special_topics/nginx.html#serving-galaxy-at-a-sub-directory-such-as-galaxy</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody">.
<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">> 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<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">>[filter:proxy-prefix]<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">>use = egg:PasteDeploy#prefix<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">>prefix = /galaxy<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">>[app:main]<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">>filter-with = proxy-prefix<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">>cookie_path = /galaxy<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">Note in your case prefix would need to be /node/m3n08/8080.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">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.<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">Also, if you get this working could you share how you did it?<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">Thanks,<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">Eric<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">---<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">Eric Franz, Senior Web & Interface App Engineer<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">Ohio Supercomputer Center<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">An Ohio Technology Consortium (OH-TECH) Member<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">1224 Kinnear Road<o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">Columbus, OH 43212<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">email:
</span><a href="mailto:efranz@osc.edu" target="_blank"><span style="mso-bookmark:_MailOriginalBody">efranz@osc.edu</span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"><b><span style="font-size:12.0pt;color:black">From:
</span></b></span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;color:black">OOD-users <</span></span><a href="mailto:ood-users-bounces@lists.osc.edu" target="_blank"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt">ood-users-bounces@lists.osc.edu</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><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 style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt">shawn.doughty@tufts.edu</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><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 style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt">ood-users@lists.osc.edu</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><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 style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt">ood-users@lists.osc.edu</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:12.0pt;color:black">><br>
<b>Subject: </b>[OOD-users] OnDemand Galaxy</span><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">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.<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">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"<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">view.html.erb is using <form action="/node/<%= host %>/<%= port %>" method="post" target="_blank"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">I can get to the port manually from another node via lynx, etc.<br clear="all">
<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"><br>
-- <o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:Helvetica">Shawn G. Doughty<br>
Manager - Research Computing</span><br>
</span><span style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:Helvetica">Tufts Technology Services (TTS)</span><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">Research Technology (RT)<o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="mso-bookmark:_MailOriginalBody">16 Dearborn Road<br>
Somerville, MA 02144</span><span style="mso-bookmark:_MailOriginalBody"><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 style="mso-bookmark:_MailOriginalBody"><span style="font-size:10.0pt;font-family:Helvetica">http://it.tufts.edu/</span></span><span style="mso-bookmark:_MailOriginalBody"></span></a><span style="mso-bookmark:_MailOriginalBody"><o:p></o:p></span></p>
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