[ensembl-dev] docker image request for REST server

[Stefano Giorgetti]

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
>
>
>
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