[ensembl-dev] Installing local copy of emsembl

[Ewan Birney]

More importantly, you don't have to use the Registry to get a  
DBAdaptor. A DBAdaptor can be
attached to a specific database directly without the Register. Check  
out the documentation
on (I think....)

   Bio::EnsEMBL::DBSQL::DBAdaptor

someone from core should probably confirm!

On 27 Oct 2010, at 09:31, Andy Yates wrote:

> 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.
>
> Regards,
>
> Andy
>
> 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
>>
>> _______________________________________________
>> Dev mailing list
>> Dev at ensembl.org
>> http://lists.ensembl.org/mailman/listinfo/dev
>
> -- 
> 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/
>
>
>
>
>
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev