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.