diff --git a/modules/Bio/EnsEMBL/Analysis/Hive/RunnableDB/ProcessGCA.pm b/modules/Bio/EnsEMBL/Analysis/Hive/RunnableDB/ProcessGCA.pm index 6ca4d6391..2fb2043f5 100644 --- a/modules/Bio/EnsEMBL/Analysis/Hive/RunnableDB/ProcessGCA.pm +++ b/modules/Bio/EnsEMBL/Analysis/Hive/RunnableDB/ProcessGCA.pm @@ -296,9 +296,6 @@ sub fetch_input { my $core_dbname = $self->param('dbowner') . '_' . $production_gca . '_core_' . $ensembl_release . '_1'; $core_db_details->{'-dbname'} = $core_dbname; - my $otherfeatures_db_details = $self->param('otherfeatures_db'); - my $otherfeatures_dbname = $self->param('dbowner') . '_' . $production_gca . '_otherfeatures_' . $ensembl_release . '_1'; - $otherfeatures_db_details->{'-dbname'} = $otherfeatures_dbname; my $rnaseq_summary_file = catfile( $short_read_dir, $production_name . '.csv' ); my $rnaseq_summary_file_genus = catfile( $short_read_dir, $production_name . '_gen.csv' ); @@ -388,10 +385,10 @@ sub fetch_input { } if ( -e $new_registry_file ) { - $self->create_registry_entry( $new_registry_file, $core_db_details, $otherfeatures_db_details, $production_name ); + $self->create_registry_entry( $new_registry_file, $core_db_details, $production_name ); } else { system( 'cp ' . $registry_file . ' ' . $new_registry_file ); - $self->create_registry_entry( $new_registry_file, $core_db_details, $otherfeatures_db_details, $production_name ); + $self->create_registry_entry( $new_registry_file, $core_db_details, $production_name ); } #Check genebuild status of assembly unless custom loading no need to check registry @@ -410,8 +407,6 @@ sub fetch_input { #Output $output_params->{'core_db'} = $core_db_details; $output_params->{'core_dbname'} = $core_dbname; - $output_params->{'otherfeatures_db'} = $otherfeatures_db_details; - $output_params->{'otherfeatures_dbname'} = $otherfeatures_dbname; $output_params->{'stable_id_start'} = $stable_id_start; $output_params->{'stable_id_prefix'} = $stable_id_prefix; $output_params->{'clade'} = $clade; @@ -681,7 +676,7 @@ sub get_clade_params { } sub create_registry_entry { - my ( $self, $registry_path, $core_db_details, $otherfeatures_db_details, $production_name ) = @_; + my ( $self, $registry_path, $core_db_details, $production_name ) = @_; unless ( -e $registry_path ) { $self->throw( "A registry file was not found on the path provided. Path:\n" . $registry_path ); @@ -696,15 +691,6 @@ sub create_registry_entry { "-species => '" . $production_name . "',\n" . "-group => 'core',\n" . ");\n"; - my $otherfeatures_string = "Bio::EnsEMBL::DBSQL::DBAdaptor->new(\n" . - "-host => '" . $otherfeatures_db_details->{'-host'} . "',\n" . - "-port => '" . $otherfeatures_db_details->{'-port'} . "',\n" . - "-dbname => '" . $otherfeatures_db_details->{'-dbname'} . "',\n" . - "-user => '" . $otherfeatures_db_details->{'-user'} . "',\n" . - "-pass => '" . $otherfeatures_db_details->{'-pass'} . "',\n" . - "-species => '" . $production_name . "',\n" . - "-group => 'otherfeatures',\n" . - ");\n"; open( my $in, '<', $registry_path ) or die "Can't open " . $registry_path . " for reading.\n"; @@ -717,7 +703,6 @@ sub create_registry_entry { print $out $line; if ( $line =~ /\{/ ) { print $out $core_string; - print $out $otherfeatures_string; } } close $out;