[Bioperl-pipeline] pipeline connections

[shawnh@worf.fugu-sg.org]

>I just meant that if it is a "biological" reason why it
> fails then it won't work on any node, if it is a node-specific reason,
> then all 10 would fail...

It won't be trivial to differentiate them. Unless u say that jobs that fail in the
running stage are 'biological' and those in reading/writing are node errors. Or else
u gotta parse the error files.

And it makes no difference whether u send 10 jobs to the node at once or 1 at a time if the node
is faulty. They will still end up with 10 failed jobs sooner or later. Unless we get the Pipeline
to be smarter. One way would be to have the batchsubmission object get the exit code from LSF and log
it down for each node. If it consistently displays a certain error after n-times, then log it down as disabled
and avoid sending jobs there thereafter.

shawn