Merge pull request #130 from jaredbischof/master

Bug fix to print out valid mysql commands for rna recompute.
Merge pull request #131 from jaredbischof/master

Syntax fix.
Created AWE pipeline template file for MG-RAST production pipeline.  Includes stages Preprocess, Dereplication, Screening, Gene Calling, Protein Clustering, Protein BLAT, RNA Search, RNA Clustering, RNA BLAT, Sims Annotation.  The stages that will still run within MG-RAST for the time being are QC, LoadDB, and the Done stage.
Merge branch 'master' of github.com:MG-RAST/pipeline