[Bioperl-pipeline] new feature

[kiran]

Hi All,

During my discussions with Lenny in trying to set up the pipeline here at
Cold Spring harbor, he came up with a request for a feature in pipeline
which seems quite pertinent in lot of situations. It is as follows.

After you have started running the pipeline, somewhere downstream or after
you have finished running, you realise that you have screwed up in some
analysis parameters (which could be anywhere in the flow of the pipeline)
and you need to rerun the pipeline from that stage onwards (because you
wouldnt want to re-run the entire pipeline).
This could easily happen lot of times (like during our ciona-annotation, we
got over it as we could meddle with the pipeline database, but we should get
some better way)

In terms of pipeline implementation, I can see the general abstraction as
you are able to modify the analysis somehow (script etc) and the pipeline
should be able to run from any particular analysis to another particular
analysis (some portion of the entire flow). Not sure currently what it
invloves to implement (may involve moving some of the completed jobs back to
job table, and more)
but before that, we need to evolve a correct spec for this feature and one
of us can look into this.

so i am throwing this up for discussion.. your comments...


kiran