add rat to harcoded list
Merge pull request #355 from teharrison/master

add rat to harcoded list
Merge pull request #356 from jaredbischof/master

Added options seem to fix mongo errors when talking to m5nr.
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
fix syntax errors
reduce default chunk size to process
Merge pull request #358 from teharrison/master

update to scripts for inbox actions
add format option to qc and preprocess stages incase sequence format not same as suffix, still backwards compatable
Merge branch 'master' of github.com:MG-RAST/pipeline
update usage
Merge pull request #359 from teharrison/master

add format option to qc and preprocess stages incase sequence format not same as suffix, still backwards compatable
fix fasta/fastq from being determined from file name
Merge pull request #360 from teharrison/master

fix fasta/fastq from being determined from file name
Modified script to use Berkeley DB locally rather than remote mongo server for m5nr lookup.