Merge pull request #352 from teharrison/master

add rat to bowtie2 index list
Merge pull request #353 from teharrison/master

Add bp_count to userattr of workflow
Merge pull request #354 from teharrison/master

fix cluster file parsing
Merge pull request #355 from teharrison/master

add rat to harcoded list
Added options seem to fix mongo errors when talking to m5nr.
Unpacking database certificates as user that is running the command.  Also, not deleting these files after task completion for the time being.
Merge pull request #356 from jaredbischof/master

Added options seem to fix mongo errors when talking to m5nr.
Removed option that causes client failure to connect to mongodb.
Merge pull request #357 from jaredbischof/master

Removed option that causes client failure to connect to mongodb.
update to scripts for inbox actions
Merge branch 'master' of github.com:teharrison/pipeline
Merge branch 'master' of github.com:MG-RAST/pipeline