[ensembl-dev] DB access for EnsemblMetazoa

Andy Yates ayates at ebi.ac.uk
Wed Dec 9 09:20:44 GMT 2020


Hi Keiran,

There's a simple answer here, that the e100 version non-vert databases are missing from the public sql server. We're looking into the why,  what we can do to recover this and get you back on track. In the intermediate time if there's a particular database you're after, you can download and load the e100 (same as release 47) metazoan DBs from here:

ftp://ftp.ensemblgenomes.org/pub/release-47/metazoa/mysql/

Or switch to a later version such as 101 or 102. Obviously if you're wanting something from all release 100 metazoa DBs, then any of those last 3 options won't be a viable.

Andy

------------
Andrew Yates - Genomics Technology Infrastructure Team Leader
The European Bioinformatics Institute (EMBL-EBI)
Wellcome Genome Campus
Hinxton, Cambridge
CB10 1SD, United Kingdom
Tel: +44-(0)1223-492538
Fax: +44-(0)1223-494468
Skype: andy.yates.ebi
http://www.ebi.ac.uk/
http://www.ensembl.org/

> On 8 Dec 2020, at 17:00, Keiran Raine <kr2 at sanger.ac.uk> wrote:
> 
> Hi,
>  
> I'm looking for some assistance reading data from the ensembl mysql instance for EnsemblMetazoa.
>  
> I have a very simple API script based on examples from the official documentation (attached), it works fine for listing the available DB adaptors via "get_all_DBAdaptors" if I point it at the vertebrate instance, but for the non-vertebrate genomes I get an empty list (registry as described here).
>  
> If nothing else, I'm just looking for someone to confirm they see the same behaviour as me when using the documented connection details.
>  
> P.s. the general ensembl instance is very slow, it was usable earlier today, not so much now.  I also did a host lookup of the database hosts, both derive down to the same IP address via a chain of aliases, so it looks like it's the port that is more important.
>  
> Thanks,
>  
> Keiran Raine, M.Sc., MBCS
> Principal Software Developer
> Cancer, Ageing and Somatic Mutation
> Wellcome Sanger Institute
>  
> kr2 at sanger.ac.uk
> Office: D3-19
> Ext: 4983
>  
> Please note that due to childcare requirements due to covid restrictions I am generally not available after 4pm.
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