#2 Object Abstraction
We need to migrate Solexa-specific behavior into SolexaPipline.pm and keep the objects it calls very generic. For example, I should be able to call the blat or rsync objects from other scripts with minimal effort. These should be de-coupled from the particulars of the SolexaPipeline as much as possible to make it easier to support other sequencers in the future. For example, things like the validators have hard coded assumptions about file names. When it's not possible/practical to migrate very specific behavior the objects should be subclassed e.g. make a SolexaValidator object that inherits from the Validator object. Also, Solexa or Nelsonlab-specific logic should be encapsulated into the SolexaPipeline and NelsonLabSolexaPipeline respectively. That means the run_pipeline and other scripts become very simple and are just used to record db status information.
Jordan, we can think more about these issues in the 2.0 release when we support other sequencers.