# ---------------------------[the following methods will be overridden by specific pipelines]-------------------------
...
...
@@ -156,49 +157,16 @@ sub pipeline_analyses {
# ---------------------------------[now comes the interfacing stuff - feel free to call but not to modify]--------------------
my$undef_const='-=[UnDeFiNeD_VaLuE]=-';# we don't use undef, as it cannot be detected as a part of a string
=head2 new
Description : Just a trivial constructor for this type of objects.
Caller : init_pipeline.pl or any other script that will drive this module.
=cut
sub new{
my($class)=@_;
my$self=bless{},$class;
return$self;
}
=head2 o
Description : This is the method you call in the interface methods when you need to substitute an option: $self->o('password') .
To reach down several levels of a multilevel option (such as $self->('pipeline_db') ) just list the keys down the desired path: $self->o('pipeline_db', '-user') .
=cut
sub o{# descends the option hash structure (vivifying all encountered nodes) and returns the value if found
Description : The method that uses the Hive/EnsEMBL API to actually create all the analyses, jobs, dataflow and control rules and resource descriptions.