Merge pull request #181 from jaredbischof/master

Changed job_num to job_id for annotation stage of pipeline so that users...
add refdb urls in job template (for refdb downloading at runtime)
Merge branch 'master' of github.com:wtangiit/pipeline
Merge branch 'master' of https://github.com/MG-RAST/pipeline
Merge pull request #182 from wtangiit/master

add refdb urls in job template (for refdb downloading at runtime)
added md5sum to error output
Merge pull request #183 from jaredbischof/master

Added e-value cutoff for protein sims and updated download_from_awe stage to have ability to download large files.
fix out of scope variable
Merge pull request #184 from teharrison/master

fix out of scope variable
Added external reference ID field to AWE workflow as xref
Merge branch 'master' of github.com:MG-RAST/pipeline