[ensembl-dev] Load homo_sapiens_core_83_37 and homo_sapiens_core_83_38 databases on same sql server?

[Luke Goodsell]

Thank you, Magali. That's very helpful.

Kind regards,
Luke

From: dev-bounces at ensembl.org [mailto:dev-bounces at ensembl.org] On Behalf Of mag
Sent: 15 March 2016 08:42
To: dev at ensembl.org
Subject: Re: [ensembl-dev] Load homo_sapiens_core_83_37 and homo_sapiens_core_83_38 databases on same sql server?

Hi Luke,

The registry can only deal with one core database for one species and release at a time.
It currently does not distinguish based on the assembly.
So if you use the API with the registry ($registry->load_registry_from_db), you will not be able to have two versions of the same species database.

However, if you explicitly connect to one database, it is possible.
For example:
my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
   -HOST => 'ensembldb.ensembl.org',
   -PORT => 3306,
   -USER => 'anonymous',
   -SPECIES => 'homo_sapiens_38',
   -DBNAME => 'homo_sapiens_core_84_38',
   -GROUP => 'core'
);
will create a database adaptor for the GRCh38 human database.
and
my $dba = Bio::EnsEMBL::DBSQL::DBAdaptor->new(
   -HOST => 'ensembldb.ensembl.org',
   -PORT => 3337,
   -USER => 'anonymous',
   -SPECIES => 'homo_sapiens_37',
   -DBNAME => 'homo_sapiens_core_84_37',
   -GROUP => 'core'
);
will create a database adaptor for the GRCh37 human database.
You can then use both databases within the same code.

Note here that I named the species homo_sapiens_38 and homo_sapiens_38, otherwise the new adaptor will supersed the old one.
Similarly, if you also have a load_registry_from_db call in your code, this will have already loaded a human core database and that will be the one used by default.

If you do not use the two databases within the same code, you can simply keep the homo_sapiens species alias, although again, without another load_registry_from_db call.


Hope that helps,
Magali
On 14/03/2016 20:46, Luke Goodsell wrote:

Hi,



Is it possible to load both the same releases of the GRCh37 and GRCh38 EnsEMBL databases on the same server and choose which assembly to use in the Perl API? We currently have them running on different mysqld instances, but this is undesirable.



I understand I could keep release n of 38 and release n-1 of 37, and load the corresponding perl modules, but this would quickly become a nightmare to maintain as new releases come out.



Kind regards,

Luke








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