[ensembl-dev] Installing local copy of emsembl

[Andreas Kahari]

On Wed, Oct 27, 2010 at 11:22:16AM +0100, Andreas Kahari wrote:
> This is all correct.  See e.g. the attached code.

To be totally correct, my example code should have used the '-species'
and '-group' switches when creating the DBAdaptor to specify that this
database was a homo_sapiens (-species) core (-group) database.  I could
then create another DBAdaptor for the variation database, set its
-species to 'homo_sapiens' and use -group to specify that this is in
fact a 'variation' database.

Andreas

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