[ensembl-dev] Setting up a local cached instance of VEP REST API

[Kieron Taylor]

Hi Cyriac,

The mirror sites don't contain clones of every database we use, just the regular stuff. If you look in your server log/console output you should get a stack trace that will help us see what is missing. Alternatively the server can be started in debug mode with -d via /script/ensembl-rest-server.pl . Otherwise you can find the log4perl configuration and raise the logging level to debug or similar.

In any case, the REST server will not work any better than our public one if you are using a distant server mirror. Ensembl performance is affected strongly by latency between database and host. It is best for us and you if you can make a local copy of the appropriate databases (i.e. you only need species that you're going to query, plus a collection of general tables). 

You can acquire dumps of the database tables here: ftp://ftp.ensembl.org/pub/release-84/mysql/

There are still be some hurdles to go, but we'll help you if we can.


Kieron


Kieron Taylor PhD.
Ensembl Developer

EMBL, European Bioinformatics Institute






> On 30 May 2016, at 22:00, Cyriac Kandoth <kandoth at cbio.mskcc.org> wrote:
> 
> Hi devs,
> 
> I'm trying to set up a local cached instance of the VEP REST API, and this link has been very helpful - https://github.com/Ensembl/ensembl-rest/wiki/REST-Installation-and-Development
> 
> I modified those instructions for CentOS and this is where I am right now - https://gist.github.com/ckandoth/a7bb6b79964926ed4263b0c869d97a96
> 
> The following command works if ensembl_rest.conf contains host = ensembldb.ensembl.org
> 
> > curl -L http://localhost:3000/info/ping?content-type=application/json
> {"ping":1}
> 
> Q1. If I set host = useastdb.ensembl.org instead, then it returns:
> 
> {"error":"Database is unavailable"}
> 
> Q2. Did I properly install the VEP REST service using the gist above?
> 
> Q3. Instead of using the remote database, I was trying to set up a local instance of everything. Can you point me the right way?
> 
> Thanks!
> 
> ~Cyriac
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