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The Job Submission daemon is a separate project in GLAST CVS, with some documentation available here.
Strictly speaking the pipeline server can work with anything that extends the JobControlClient class, which allows jobs to be submitted, queried for their status, and canceled. In practice only a couple of classes in the implementation of the job control client depend on LSF, so we expect remote sites to run a modified version of the standard JobControlClient. The classes which depend on LSF are:

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