Merge pull request #157 from wtangiit/master

awe_preprocess and awe_dereplicate retaining .remove.fna
Merge pull request #158 from wtangiit/master

depreciated cmd option for old pipeline templates
Added log msg.
Added code to insert job into AWE MGRAST lookup database when submitting job to AWE.  This will be used in the short term to track which jobs have been submitted to AWE that have not yet completed.
Merge pull request #159 from jaredbischof/master

Added code to insert job into AWE MGRAST lookup database when submitting to AWE.
Typo.
Merge pull request #160 from jaredbischof/master

Typo.
Wrong variable was inserting into AWE MGRAST lookup db.
Merge pull request #161 from jaredbischof/master

Minor bug fix.
Added two of the removed.fna files to the files being downloaded from Shock after the AWE workflow is complete.  These files are needed for stats computations in the done stage.
Merge pull request #162 from jaredbischof/master

Added 2 files to download from Shock after AWE workflow is complete.
Added awe_url to AWE_MGRAST lookup database.
Created script that will be run by cron to get a list of jobs from the AWE MGRAST lookup database and submit the completed jobs to the rest of the MG-RAST pipeline.
Merge pull request #163 from jaredbischof/master

 Created script that will be run by cron to get a list of jobs from the AWE MGRAST lookup database and submit the completed jobs to the rest of the MG-RAST pipeline.
Typo
Merge pull request #164 from jaredbischof/master

Typo
Fixing permissions
Merge pull request #165 from jaredbischof/master

Fixing permissions
Fixing bugs.
Merge pull request #166 from jaredbischof/master

Fixing bugs.