Merge pull request #151 from jaredbischof/master

Edited pipeline_annotation stage so it should allow for empty aa sims or rna sims file, but not both.
Merge pull request #152 from jaredbischof/master

Edited sims2annotation so that it too should now handle an empty aa sims or rna sims file, but not both.
Merge pull request #153 from jaredbischof/master

Edits to get pipeline to run in AWE.
Merge pull request #154 from jaredbischof/master

Fixing uninitialized value.
Merge pull request #155 from jaredbischof/master

Finalizing stuff to handle running part of the pipeline in AWE.
Merge pull request #156 from jaredbischof/master

Syntax errors.
Merge branch 'master' of github.com:wtangiit/pipeline
Merge branch 'master' of https://github.com/MG-RAST/pipeline
make awe_preprocess and awe_dereplicate retaining .remove.fna
Merge pull request #157 from wtangiit/master

awe_preprocess and awe_dereplicate retaining .remove.fna
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.