[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 :
http://www.ensembl.org/info/docs/api/api_installation.html
Your help is most appreciated.
Best regards,
Duarte
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
API
#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();
printf(
"species/group\t%s/%s\ndatabase\t%s\nhost:port\t%s:%s\n\n",
$db_adaptor->species(), $db_adaptor->group(),
$db_connection->dbname(), $db_connection->host(),
$db_connection->port()
);
}
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