[ensembl-dev] Installing local copy of emsembl

[Andreas Kahari]

This is all correct.  See e.g. the attached code.


Andreas


On Wed, Oct 27, 2010 at 11:06:57AM +0100, Ewan Birney wrote:
> 
> 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
> 
> 
> _______________________________________________
> Dev mailing list
> Dev at ensembl.org
> http://lists.ensembl.org/mailman/listinfo/dev
> 

-- 
Andreas Kähäri, Ensembl Software Developer
European Bioinformatics Institute (EMBL-EBI)
Wellcome Trust Genome Campus
Hinxton, Cambridge CB10 1SD, United Kingdom
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