Commit 3e5a2101 authored by Leo Gordon's avatar Leo Gordon
Browse files

support multiple -pipeconfig options (each applied on top of the previous state of the graph)

parent 75bc0132
......@@ -34,7 +34,7 @@ sub main {
'reg_alias|reg_name=s' => \$self->{'reg_alias'},
'nosqlvc=i' => \$self->{'nosqlvc'}, # using "=i" instead of "!" for consistency with scripts where it is a propagated option
'pipeconfig|pc=s' => \$self->{'pipeconfig'},
'pipeconfig|pc=s@' => \$self->{'pipeconfigs'}, # now an array
'f|format=s' => \$self->{'format'},
'o|out|output=s' => \$self->{'output'},
......@@ -77,13 +77,15 @@ sub main {
Bio::EnsEMBL::Hive::DBSQL::DBAdaptor->init_collections();
}
if($self->{'pipeconfig'}) {
my $pipeconfig_package_name = load_file_or_module( $self->{'pipeconfig'} );
if($self->{'pipeconfigs'}) {
foreach my $pipeconfig (@{ $self->{'pipeconfigs'} }) {
my $pipeconfig_package_name = load_file_or_module( $pipeconfig );
my $pipeconfig_object = $pipeconfig_package_name->new();
$pipeconfig_object->process_options( 0 );
my $pipeconfig_object = $pipeconfig_package_name->new();
$pipeconfig_object->process_options( 0 );
$pipeconfig_object->add_objects_from_config();
$pipeconfig_object->add_objects_from_config();
}
}
my $graph = Bio::EnsEMBL::Hive::Utils::Graph->new( $self->{'dba'} );
......@@ -104,7 +106,7 @@ __END__
=head1 SYNOPSIS
./generate_graph.pl -url mysql://user:pass@server:port/dbname -output OUTPUT_LOC [-help]
./generate_graph.pl [ -url mysql://user:pass@server:port/dbname ] [-pipeconfig TopUp_conf.pm]* -output OUTPUT_LOC [-help]
=head1 DESCRIPTION
......@@ -128,6 +130,11 @@ B<--reg_alias>
species/alias name for the Hive DBAdaptor
B<--pipeconfig>
A pipeline configuration file that can function both as the initial source of pipeline structure or as a top-up config.
This option can now be used multiple times for multiple top-ups.
B<--output>
Location of the file to write to.
......
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