view variant_effect_predictor/Bio/EnsEMBL/Utils/ensembl_init.example @ 3:d30fa12e4cc5 default tip

Merge heads 2:a5976b2dce6f and 1:09613ce8151e which were created as a result of a recently fixed bug.

#
# Example of configuration file used by Bio::EnsEMBL::Registry::load_all
# method to store/register all kind of Adaptors.

use strict;
use warnings;

use Bio::EnsEMBL::Utils::ConfigRegistry;
use Bio::EnsEMBL::DBSQL::DBAdaptor;
use Bio::EnsEMBL::Compara::DBSQL::DBAdaptor;

my @aliases;

new Bio::EnsEMBL::DBSQL::DBAdaptor(
                                 '-host'    => 'ensembldb.ensembl.org',
                                 '-user'    => 'anonymous',
                                 '-port'    => '3306',
                                 '-species' => 'Homo sapiens',
                                 '-group'   => 'core',
                                 '-dbname' => 'homo_sapiens_core_23_34e'
);

@aliases = ( 'H_Sapiens',    'homo sapiens',
             'Homo_Sapiens', 'Homo_sapiens',
             'Homo',         'homo',
             'human' );

Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
                                           '-species' => 'Homo sapiens',
                                           '-alias'   => [@aliases] );

new Bio::EnsEMBL::DBSQL::DBAdaptor(
                                 '-host'    => 'ensembldb.ensembl.org',
                                 '-user'    => 'anonymous',
                                 '-port'    => '3306',
                                 '-species' => 'Mus musculus',
                                 '-group'   => 'core',
                                 '-dbname' => 'mus_musculus_core_23_32c'
);

@aliases = ( 'M_Musculus',   'mus musculus',
             'Mus_Musculus', 'Mus_musculus',
             'Mus',          'mus',
             'mouse' );

Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
                                           '-species' => 'Mus musculus',
                                           '-alias'   => [@aliases] );

new Bio::EnsEMBL::DBSQL::DBAdaptor(
                             '-host'    => 'ensembldb.ensembl.org',
                             '-user'    => 'anonymous',
                             '-port'    => '3306',
                             '-species' => 'Rattus norvegicus',
                             '-group'   => 'core',
                             '-dbname' => 'rattus_norvegicus_core_23_3c'
);

@aliases = ( 'R_Norvegicus',      'rattus norvegicus',
             'Rattus_Norvegicus', 'Rattus_norvegicus',
             'Rattus',            'rattus',
             'rat' );

Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
                                      '-species' => 'Rattus norvegicus',
                                      '-alias'   => [@aliases] );

new Bio::EnsEMBL::Compara::DBSQL::DBAdaptor(
                                     '-host' => 'ensembldb.ensembl.org',
                                     '-user' => 'anonymous',
                                     '-port' => '3306',
                                     '-species' => 'Compara23',
                                     '-dbname' => 'ensembl_compara_23_1'
);

@aliases = ( 'ensembl_compara_23_1', 'compara23' );

Bio::EnsEMBL::Utils::ConfigRegistry->add_alias(
                                              '-species' => 'Compara23',
                                              '-alias'   => [@aliases]
);

1;