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<p>Hello Duarte,</p>
<p>That's weird. It looks like the configuration is missing.</p>
<p>I can suggest to</p>
<ul>
<li>run the container and log in with interactive session</li>
<li>you should land at "/opt/ensembl-rest"; if not, "cd" into
there</li>
<li>check where a file "ensembl_rest.conf" is there or not (I
guess not)</li>
<li>assuming this file is missing</li>
<ul>
<li>cp ensembl_rest.conf.default ensembl_rest.conf</li>
<li>you may want to change the default ensembl version (from 88
to 109 ... or whatever you are interested in)</li>
<ul>
<li>you may need to install a text editor</li>
</ul>
<li>temporarily you may want to switch the debug mode on - pls,
see
<a class="moz-txt-link-freetext" href="https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development">https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development</a>
under section "Application Debugging"<br>
</li>
<li>./script/ensembl_rest_server.pl --port 80</li>
<li>amend the Dockerfile to comprise these changes above and
re-build the image</li>
<li>pls, confirm my guessing was right ;-) ... or not :-(</li>
</ul>
</ul>
<p>Best,</p>
<p>S<br>
</p>
<div class="moz-cite-prefix">On 02/05/2023 14:03, Duarte Molha
wrote:<br>
</div>
<blockquote type="cite"
cite="mid:CAGqkoELZvGOMgWSMmOxYjDdaeWpZYG=gtLmYQD28tgZHY0ekBA@mail.gmail.com">
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<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>
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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"
moz-do-not-send="true" class="moz-txt-link-freetext">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>
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<br>
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<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"
moz-do-not-send="true" class="moz-txt-link-freetext">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"
moz-do-not-send="true" class="moz-txt-link-freetext">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" moz-do-not-send="true"
class="moz-txt-link-freetext">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" moz-do-not-send="true"
class="moz-txt-link-freetext">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" moz-do-not-send="true"
class="moz-txt-link-freetext">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" moz-do-not-send="true"
class="moz-txt-link-freetext">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" moz-do-not-send="true"
class="moz-txt-link-freetext">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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