[ensembl-dev] Local V64 instalation

[ian Longden]

Check
/ensembl/v64/ensembl-api/ensembl/modules/Bio/EnsEMBL/ApiVersion.pm

and make sure that this has:
my $API_VERSION = 64;


The script seems to think it is release 63. You may need to checkout
from cvs release 64 again.

-Ian.


On Wed, Oct 19, 2011 at 10:25 AM, Duarte Molha <duartemolha at gmail.com> wrote:
> 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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