[ensembl-dev] Installing local copy of emsembl

Andrea Edwards edwardsa at cs.man.ac.uk
Tue Oct 26 23:48:33 BST 2010


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';

     -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();

         $db_adaptor->species(),   $db_adaptor->group(),
         $db_connection->dbname(), $db_connection->host(),

Many thanks

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