sub run {
my ($self) = @_;
my $dbas = {};
my $species = $self->param_required('species');
return if $species eq 'Ancestral sequences';
$log->info("Finding DBAdaptors for $species");
for my $type (qw/core variation otherfeatures funcgen/) {
$dbas->{$type} = $self->get_DBAdaptor($type);
}
$log->info("Connecting to info database");
my $dba =
Bio::EnsEMBL::MetaData::DBSQL::MetaDataDBAdaptor->new(
-USER =>,
$self->param('info_user'),
-PASS =>,
$self->param('info_pass'),
-HOST =>,
$self->param('info_host'),
-PORT =>,
$self->param('info_port'),
-DBNAME =>,
$self->param('info_dbname')
);
my $gdba = $dba->get_GenomeInfoAdaptor();
# set the release to use when storing genomes
my $rdba = $dba->get_DataReleaseInfoAdaptor();
my $release;
if ( defined $self->param('eg_release') ) {
$release =
$rdba->fetch_by_ensembl_genomes_release(
$self->param('eg_release') );
}
else {
$release =
$rdba->fetch_by_ensembl_release( $self->param('release') );
}
$gdba->data_release($release);
my $upd = $self->param('force_update') || 0;
my $opts = { -INFO_ADAPTOR => $gdba,
-ANNOTATION_ANALYZER =>
Bio::EnsEMBL::MetaData::AnnotationAnalyzer->new(),
-COMPARA => 0,
-CONTIGS => $self->param('contigs') || 1,
-FORCE_UPDATE => $upd,
-VARIATION => $self->param('variation') || 1 };
my $processor =
Bio::EnsEMBL::MetaData::MetaDataProcessor->new(%$opts);
$log->info("Processing $species");
my $md = $processor->process_genome($dbas);
if ( defined $md->dbID() && $upd == 1 ) {
$log->info( "Updating " . $md->name() );
$gdba->update($md);
}
elsif ( !defined $md->dbID() ) {
$log->info( "Storing " . $md->name() );
$gdba->store($md);
}
$log->info("Completed processing $species");
return;
} ## end sub run
Code:
