<div dir="ltr">Dear Stefano<div><br></div><div>I was able to build the image.<br><br>but it does not run.<br><br>you did not have this issue on your test?<br><br>docker run ensembl-rest<br>Getopt::Long::Descriptive was configured with these ambiguous options: h<br>You must configure a default store type unless you use exactly one store plugin. at /usr/share/perl5/Catalyst/Plugin/ConfigLoader.pm line 101.<br>Compilation failed in require at /usr/share/perl5/Catalyst/Utils.pm line 309.</div><div><div><div dir="ltr" class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div dir="ltr"><br></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, 27 Apr 2023 at 16:20, Duarte Molha <<a href="mailto:duartemolha@gmail.com">duartemolha@gmail.com</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><div dir="ltr">Appreciate it Stefano<br><br>I understand your concerns. I have a fast connection to the underlying database as it is all hosted in the same place. <br>This is not for general (public) consumption, only for internal use <br><br>But this is a great starting point<div><br></div><div>Many thanks</div><div><br></div><div>Duarte<br clear="all"><div><div dir="ltr"><div dir="ltr"><div dir="ltr"><br></div></div></div></div><br></div></div><br><div class="gmail_quote"><div dir="ltr" class="gmail_attr">On Thu, 27 Apr 2023 at 16:11, Stefano Giorgetti <<a href="mailto:sgiorgetti@ebi.ac.uk" target="_blank">sgiorgetti@ebi.ac.uk</a>> wrote:<br></div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<p>Dear Duarte,</p>
<p>Thanks for your email.</p>
<p>From my perspective, the installation procedure is (sort of) OK:
there are a few minor inaccuracies (e.g. expected directory
structure, PERL5LIB setup) and sub-optimal steps (e.g. Tabix, use
of cpanm instead of pre-compiled packages), but not essential
ones.</p>
<p>Carried it out, just in case, and can confirm I could fire up a
REST server instance in both a VM and Docker container.<br>
TBH, I started from scratch, as not familiar with <a href="https://github.com/genomehubs/ensembl-rest-docker" target="_blank">https://github.com/genomehubs/ensembl-rest-docker</a></p>
<p>This said, I am not sure I can bless and recommend your approach.<br>
To achieve speed, you may also want to have fast connection to the
underlying DBs; not to mention good tuning and configuration of
the web server.<br>
Deployment of REST server in a Production environment is not a
trivial task.</p>
<p>However, I am not aware of the specificities of your use case(s)
and environment, and can hardly advise.</p>
<p>Finally, please find attached the Dockerfile I used, which -
although neither complete nor optimised - may serve you as a
reference.</p>
<p>Best wishes,</p>
<p>Stefano<br>
</p>
<p><br>
</p>
<div>On 25/04/2023 11:16, Duarte Molha
wrote:<br>
</div>
<blockquote type="cite">
<div dir="ltr">
<div dir="ltr">
<div>I have tried unsuccessfully to create a ENSEMBL REST
server docker container to run locally on my
locally installed ensembl database.</div>
<div><br>
</div>
<div>I tried to follow the instructions here:<br>
<br>
<a href="https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development" target="_blank">https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development</a><br>
<br>
It has not worked.<br>
<br>
The links for Catalyst are broken:</div>
<ul>
<li style="box-sizing:border-box"><a href="http://wiki.catalystframework.org/wiki/installation" rel="nofollow" style="box-sizing:border-box;background-color:transparent;text-decoration-line:none" target="_blank">http://wiki.catalystframework.org/wiki/installation</a> (basic)</li>
<li style="box-sizing:border-box;margin-top:0.25em"><a href="http://wiki.catalystframework.org/wiki/installingcatalyst" rel="nofollow" style="box-sizing:border-box;background-color:transparent;text-decoration-line:none" target="_blank">http://wiki.catalystframework.org/wiki/installingcatalyst</a> (advanced)<br>
</li>
</ul>
<div><font face="-apple-system, BlinkMacSystemFont, Segoe UI,
Noto Sans, Helvetica, Arial, sans-serif, Apple Color
Emoji, Segoe UI Emoji" color="#1f2328"><span style="font-size:16px">I am able to install it by using
CPAN, but it might be part of why I have been
unsuccessful.<br>
<br>
I forked a github project that tries to do this:<br>
<br>
</span></font><a href="https://github.com/genomehubs/ensembl-rest-docker" target="_blank">https://github.com/genomehubs/ensembl-rest-docker</a><br>
<font face="-apple-system, BlinkMacSystemFont, Segoe UI,
Noto Sans, Helvetica, Arial, sans-serif, Apple Color
Emoji, Segoe UI Emoji" color="#1f2328"><span style="font-size:16px"><br>
and modified it to work with human species...<br>
<br>
</span></font><a href="https://github.com/duartemolha/ensembl-rest-docker" target="_blank">https://github.com/duartemolha/ensembl-rest-docker</a><br>
<br>
But it still is not working</div>
<div><br>
</div>
<div>Either some hints on what is wrong with my code or
(better yet) a pre-build version of your rest server
containerised would be greatly appreciated<br>
<br>
The main reason I am doing this is because I am developing
some apps that I will want to do many (fast) queries and I
do not want to rely on ensembl servers to get this as I will
be rate limited pretty sharpish :)<br>
<br>
Many thanks</div>
<div><br>
</div>
<div>Duarte</div>
<div><br>
</div>
<div><br>
</div>
</div>
</div>
<br>
<fieldset></fieldset>
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