Merge pull request #276 from teharrison/develop

bug fixes and updates
Merge pull request #277 from teharrison/develop

bug fixes and updates
Merge pull request #278 from teharrison/develop

fix file name error
Merge pull request #279 from teharrison/develop

fix wrong subroutine
Merge pull request #280 from teharrison/develop

update rna search, add hit start/stop to fasta header
Merge branch 'develop' of git://github.com/MG-RAST/pipeline into develop
fix template args