Merge pull request #132 from jaredbischof/master

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

Fixed typo in mg-rast awe job template.
Merge pull request #134 from jaredbischof/master

Script to submit MG-RAST jobs to AWE.
Merge pull request #135 from jaredbischof/master

Tested, debugged, and polished up script to submit jobs to Shock and AWE.  It works.
Merge pull request #136 from jaredbischof/master

Updates to pipeline_submit_to_awe and pipeline_annotation.
Merge pull request #137 from jaredbischof/master

Edited error checking to allow some of the input files to be empty.
Merge pull request #138 from jaredbischof/master

Syntax fix.
awe_wrapper following naming convention of mg-rast jobs
Merge pull request #140 from jaredbischof/master

Fixed prefix for annotation stage output files.
Merge pull request #139 from wtangiit/master

update in awe_cluster_parallel.pl for naming convention
mgrast-prod.awe.template
updates in awe_wrappers for matched cmd line argument names
Merge pull request #141 from wtangiit/master

updates in awe_templates and awe wrappers
Merge pull request #142 from jaredbischof/master

Added download of files from Shock after successul completion of AWE pipeline with error checking.
awe_dereplicate.pl specifies sorting dir to cwd
making awe_cluster_parallel.pl skippable when fails
Merge pull request #143 from wtangiit/master

updates in awe wrapper tasks
Merge pull request #144 from jaredbischof/master

Edited AWEUtil to make smaller chunks based on sequence lengths and added it to pipeline repo.
Merge pull request #145 from jaredbischof/master

Edited pipeline_loadAWE to use pipeline/bin/AWEUtil version.
Update mgrast-prod.awe.template