Merge pull request #129 from wtangiit/master

update in awe_dereplicate.pl
Bug fix to print out valid mysql commands for rna recompute.
Merge pull request #130 from jaredbischof/master

Bug fix to print out valid mysql commands for rna recompute.
Syntax fix.
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
Merge pull request #132 from jaredbischof/master

Created AWE pipeline template for MG-RAST production pipeline.
Fixed typo.
Merge pull request #133 from jaredbischof/master

Fixed typo in mg-rast awe job template.
Script to submit MG-RAST jobs to AWE.
Merge pull request #134 from jaredbischof/master

Script to submit MG-RAST jobs to AWE.
Fixed template.
Tested, debugged, and polished up script to submit jobs to Shock and AWE.  It works.
Merge pull request #135 from jaredbischof/master

Tested, debugged, and polished up script to submit jobs to Shock and AWE.  It works.
Debugging pipeline_submit_to_awe.
Removing file path to md5rna_clust variable.  Not needed or valid inside of AWE.
Edited to allow zero size rna or aa clustering files.
Merge pull request #136 from jaredbischof/master

Updates to pipeline_submit_to_awe and pipeline_annotation.
Edited error checking to allow some of the input files to be empty.