[ensembl-dev] docker image request for REST server

[Stefano Giorgetti]

Hello Duarte,

That's weird. It looks like the configuration is missing.

I can suggest to

  * run the container and log in with interactive session
  * you should land at "/opt/ensembl-rest"; if not, "cd" into there
  * check where a file "ensembl_rest.conf" is there or not (I guess not)
  * assuming this file is missing
      o cp ensembl_rest.conf.default ensembl_rest.conf
      o you may want to change the default ensembl version (from 88 to
        109 ... or whatever you are interested in)
          + you may need to install a text editor
      o temporarily you may want to switch the debug mode on - pls, see
        https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development
        under section "Application Debugging"
      o ./script/ensembl_rest_server.pl --port 80
      o amend the Dockerfile to comprise these changes above and
        re-build the image
      o pls, confirm my guessing was right ;-) ... or not :-(

Best,

S

On 02/05/2023 14:03, Duarte Molha wrote:
> Dear Stefano
>
> I was able to build the image.
>
> but it does not run.
>
> you did not have this issue on your test?
>
> docker run ensembl-rest
> Getopt::Long::Descriptive was configured with these ambiguous options: h
> You must configure a default store type unless you use exactly one 
> store plugin. at /usr/share/perl5/Catalyst/Plugin/ConfigLoader.pm line 
> 101.
> Compilation failed in require at /usr/share/perl5/Catalyst/Utils.pm 
> line 309.
>
>
>
> On Thu, 27 Apr 2023 at 16:20, Duarte Molha <duartemolha at gmail.com> wrote:
>
>     Appreciate it Stefano
>
>     I understand your concerns. I have a fast connection to the
>     underlying database as it is all hosted in the same place.
>     This is not for general (public) consumption, only for internal use
>
>     But this is a great starting point
>
>     Many thanks
>
>     Duarte
>
>
>
>     On Thu, 27 Apr 2023 at 16:11, Stefano Giorgetti
>     <sgiorgetti at ebi.ac.uk> wrote:
>
>         Dear Duarte,
>
>         Thanks for your email.
>
>         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.
>
>         Carried it out, just in case, and can confirm I could fire up
>         a REST server instance in both a VM and Docker container.
>         TBH, I started from scratch, as not familiar with
>         https://github.com/genomehubs/ensembl-rest-docker
>
>         This said, I am not sure I can bless and recommend your approach.
>         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.
>         Deployment of REST server in a Production environment is not a
>         trivial task.
>
>         However, I am not aware of the specificities of your use
>         case(s) and environment, and can hardly advise.
>
>         Finally, please find attached the Dockerfile I used, which -
>         although neither complete nor optimised - may serve you as a
>         reference.
>
>         Best wishes,
>
>         Stefano
>
>
>         On 25/04/2023 11:16, Duarte Molha wrote:
>>         I have tried unsuccessfully to create a ENSEMBL REST server
>>         docker container to run locally on my locally installed
>>         ensembl database.
>>
>>         I tried to follow the instructions here:
>>
>>         https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development
>>
>>         It has not worked.
>>
>>         The links for Catalyst are broken:
>>
>>           * http://wiki.catalystframework.org/wiki/installation (basic)
>>           * http://wiki.catalystframework.org/wiki/installingcatalyst (advanced)
>>
>>         I am able to install it by using CPAN, but it might be part
>>         of why I have been unsuccessful.
>>
>>         I forked a github project that tries to do this:
>>
>>         https://github.com/genomehubs/ensembl-rest-docker
>>
>>         and modified it to work with human species...
>>
>>         https://github.com/duartemolha/ensembl-rest-docker
>>
>>         But it still is not working
>>
>>         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
>>
>>         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 :)
>>
>>         Many thanks
>>
>>         Duarte
>>
>>
>>
>>         _______________________________________________
>>         Dev mailing listDev at ensembl.org
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>
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