Changed check for the "assembled" option in the Job database to check for the existence of the $raw_dir/$job_num.abundance file because the recompute cluster can't see the Job database.
Created separate Pipeline library for the recompute that will print sql statements to a file in the jobsv3 directory of the job that is being recomputed because it cannot access the Job database directly from the recompute cluster.
Edited stage script to use Pipeline_recompute.pm instead of Pipeline.pm.
Merge pull request #93 from jaredbischof/master

Updates for recompute.