[ensembl-dev] Installing local copy of emsembl
Andrea Edwards
edwardsa at cs.man.ac.uk
Tue Oct 26 23:48:33 BST 2010
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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