Merge pull request #203 from teharrison/master

fix variable name
Added shock parameter for overriding the Shock URL that the job results should be downloaded from.
Merge pull request #204 from jaredbischof/master

Added shock parameter for overriding the Shock URL that the job results ...
Upadtes to help text.
Added auth token for downloading jobs from Shock.
Merge pull request #205 from jaredbischof/master

Added auth token for downloading jobs from Shock.
Update to config variable name
Merge pull request #206 from jaredbischof/master

Update to config variable name
Fixing bug in md5 counts.
Merge pull request #207 from jaredbischof/master

Fixing bug in md5 counts.
Edit to specify output prefix
Adding qc stage to mgrast awe workflow.
Merge pull request #208 from jaredbischof/master

Adding QC stage to MG-RAST AWE workflow
Added download of qc stage output files to AWE workflow document.
Merge pull request #209 from jaredbischof/master

Added download of qc stage output files to AWE workflow document.
More updates to AWE template to make AWE server happy.
Merge pull request #210 from jaredbischof/master

More updates to AWE template to make AWE server happy.
match argument with the awe template
Merge pull request #211 from wtangiit/master

minor fix: match argument with the mgrast job template
add awe_preprocess_qc.pl, a script merging preprocess and qc stages to reduce data movement