[Bioperl-pipeline] job dependence

[jeremyp at sgx3.bmb.uga.edu]

Hello,

I may have sent a message before on this topic. I checked the most recent
sources, and it still seems to me that certain job dependency checking may
be missing. I haven't tested the latest code, but, in order to get my code
working with a version of the pipeline from mid-December, I added
dependency checks to runner.pl and also to the second place jobs are
spawned within PipelineManager.pl. I am using the UPDATE features of the
pipeline extensively. Am I missing something?

Jeremy