[ensembl-dev] Local V64 instalation

Duarte Molha duartemolha at gmail.com
Wed Oct 19 10:25:22 BST 2011

I am having issues using a local version of ensembl database.

I have already installed both the v62 version and the v64 version of the
ensembl database and respective APIs.

If I use v62 api I can query the database with no issues, using V64 api the
registry does not seem to read the mySQL database.

As a test I used the local v64 api to query the remote database and pull out
the tables it finds. Here are the ones I retrieve for Human:

species/group   homo_sapiens/core
database        homo_sapiens_core_63_37
host:port       ensembldb.ensembl.org:5306

species/group   homo_sapiens/cdna
database        homo_sapiens_cdna_63_37
host:port       ensembldb.ensembl.org:5306

species/group   homo_sapiens/vega
database        homo_sapiens_vega_63_37
host:port       ensembldb.ensembl.org:5306

species/group   homo_sapiens/otherfeatures
database        homo_sapiens_otherfeatures_63_37
host:port       ensembldb.ensembl.org:5306

species/group   homo_sapiens/variation
database        homo_sapiens_variation_63_37
host:port       ensembldb.ensembl.org:5306

species/group   homo_sapiens/funcgen
database        homo_sapiens_funcgen_63_37
host:port       ensembldb.ensembl.org:5306

Why is this query pulling out V63 tables? Should it not be querying the V64
tables instead? Is the current api on the server really v63 instead?
I got the API from :

Your help is most appreciated.

Best regards,


PS:  This is the script I used to query

#!/usr/bin/perl -w
use strict;

#Import Libs
use lib '/ensembl/v64/ensembl-api/ensembl/modules'; # points to HG19 ensembl

#Use ENSEMBL modules
use Bio::EnsEMBL::Registry;

my $registry = 'Bio::EnsEMBL::Registry';

#Create Registry for connecting to database
$registry->load_registry_from_db( -host => 'ensembldb.ensembl.org',
                        -user => 'anonymous');

my @db_adaptors = @{ $registry->get_all_DBAdaptors() };

foreach my $db_adaptor (@db_adaptors) {
    my $db_connection = $db_adaptor->dbc();

        $db_adaptor->species(),   $db_adaptor->group(),
        $db_connection->dbname(), $db_connection->host(),
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