[ensembl-dev] docker image request for REST server

[Duarte Molha]

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
>>
>>
>>
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>>
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