Finished bin script that doesn't produce rna sims, but just sorts and processes them.
Finished with stage script that runs a single bin script "sims_to_abundance" which processes aa and rna sims and produces abundance summaries.  All the "work" except for moving files around is now performed inside the bin scripts instead of having a lot of the processing in the load stage (pipeline_loadDB) as before.
Finished with bin script that processes aa and rna sims and takes a lot of the work out of the pipeline_loadDB script.  This script takes as primary input the aa and rna sims and cluster files and outputs the abundance summary files, the filter.seq file and the source.stats file.
Merge pull request #92 from jaredbischof/master

Finished and tested a few scripts for recompute and awe.