my ($file_or_module, $tweaks) = @_;
my $pipeconfig_package_name = load_file_or_module( $file_or_module );
my $pipeconfig_object = $pipeconfig_package_name->new();
die "PipeConfig $pipeconfig_package_name not created\n" unless $pipeconfig_object;
die "PipeConfig $pipeconfig_package_name is not a Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf\n" unless $pipeconfig_object->isa('Bio::EnsEMBL::Hive::PipeConfig::HiveGeneric_conf');
print "> Parsing the command-line options.\n\n";
$pipeconfig_object->process_options( 1 );
# Restore the password in the URL so that pipelines that need
# pipeline_url() don't see _EHIVE_HIDDEN_PASS
if ($pipeconfig_object->pipeline_url =~ /\$\{_EHIVE_HIDDEN_PASS\}/) {
my $real_password = $ENV{_EHIVE_HIDDEN_PASS};
$pipeconfig_object->root()->{'pipeline_url'} =~ s/\$\{_EHIVE_HIDDEN_PASS\}/$real_password/;
$pipeconfig_object->root()->{'pipeline_url'} =~ s/'//g;
}
print "> Running the creation commands.\n\n";
$pipeconfig_object->run_pipeline_create_commands();
my $pipeline = Bio::EnsEMBL::Hive::HivePipeline->new(
-url => $pipeconfig_object->pipeline_url(),
-no_sql_schema_version_check => !$pipeconfig_object->is_analysis_topup );
my $hive_dba = $pipeline->hive_dba()
or die "HivePipeline could not be created for ".$pipeconfig_object->pipeline_url();
$hive_dba->dbc->requires_write_access();
print "> Parsing the PipeConfig file and adding objects (this may take a while).\n\n";
$pipeconfig_object->add_objects_from_config( $pipeline );
if($tweaks and @$tweaks) {
print "> Applying tweaks.\n\n";
my ($need_write, $msg_list_ref, $json) = $pipeline->apply_tweaks( $tweaks );
$pipeconfig_object->print_debug(join("", @$msg_list_ref), "\n");
}
$pipeline->test_connections();
print "> Storing the pipeline in the database.\n\n";
$pipeline->save_collections();
print "Pipeline successfully stored at ", $pipeconfig_object->pipeline_url, " !\n\n";
print $pipeconfig_object->useful_commands_legend();
$hive_dba->dbc->disconnect_if_idle; # This is necessary because the current lack of global DBC caching may leave this DBC connected and prevent deletion of the DB in pgsql mode
return $hive_dba->dbc->url;
}
Code:
