[ensembl-dev] docker image request for REST server

[Duarte Molha]

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
>
>
>
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