Merge pull request #237 from jaredbischof/master

Removed reference to old AWE directory that no longer exists.
Merge pull request #238 from jaredbischof/master

Added exception to handle case when done stage has been run previously b...
Merge pull request #239 from jaredbischof/master

Updated to newer version of fastq-join.
Changed to auto-detect file type
Merge pull request #240 from wltrimbl/autodetect

Auto-detect file type in consensus.py
Merge pull request #241 from jaredbischof/master

Edited code to handle assembled jobs corrently and give the appropriate ...
Merge pull request #242 from jaredbischof/master

Update to split rna blat jobs.
modified awe.template for new task splitting strategies at some stages
Merge pull request #243 from wtangiit/master

modified awe.template for new task splitting strategies at some stages
Merge pull request #244 from jaredbischof/master

Fix to syntax error.
Merge pull request #245 from jaredbischof/master

Fix so that preprocessing stage completes successfully for assembled job...
added obo parser
Merge pull request #246 from jaredbischof/master

Jobs that are being split do not require the totalwork parameter and mak...
obo parser update
Merge branch 'master' of github.com:MG-RAST/pipeline
update url
update validate metadata to use mg-rast API and not bioportal API to retrieve ontology lists
remove test url
Merge pull request #247 from teharrison/master

metadata update
Merge pull request #248 from jaredbischof/master

Silent error was preventing assembled jobs from getting the proper abund...