[ensembl-dev] Installing local copy of emsembl

Andy Yates ayates at ebi.ac.uk
Wed Oct 27 09:31:45 BST 2010

Hi Andrea,

Bio::EnsEMBL::Registry uses a set of regular expressions in conjunction with the current API release to find the databases it should load from a MySQL server. It is possible to use a custom name but then you would be responsible for creating the DBAdaptor instance not Bio::EnsEMBL::Registry.



On 26 Oct 2010, at 23:48, Andrea Edwards wrote:

> Hi
> When you create a local copy of the ensembl database, what do you call the database? For example I want to create a database for the cow core and variation data. Do i call them, for example, bos_taurus_core_59_4h, which is the name of the latest release of the core database? Otherwise I dont know how the Perl API will know the name of the database to connect to. Perhaps I missed this is the readme but I couldn't find it. Perhaps its too obvious to specify!
> If i run the script below it prints out the database name given above for cow so I presume that's the one you use.
> my $reg = 'Bio::EnsEMBL::Registry';
> $reg->load_registry_from_db(
>    -host => 'ensembldb.ensembl.org',
>    -user => 'anonymous'
> );
> my @db_adaptors = @{ $reg->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()
>    );
> }
> Many thanks
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Andrew Yates                   Ensembl Genomes Engineer
EMBL-EBI                       Tel: +44-(0)1223-492538
Wellcome Trust Genome Campus   Fax: +44-(0)1223-494468
Cambridge CB10 1SD, UK         http://www.ensemblgenomes.org/

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