Merge pull request #182 from wtangiit/master

add refdb urls in job template (for refdb downloading at runtime)
added md5sum to error output
Adding 1.0e-03 e-value cutoff so blat results.
Edits to enable script to download large files from Shock that cannot fit into system memory before printing the downloaded file to disk.
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
Merge pull request #185 from jaredbischof/master

Added external reference ID field to AWE workflow
Added code to retry a Shock download N times if it fails or the byte size or md5 checksum does not match what is in Shock, where N is a global variable in the script.  Also, added code to check file byte size before md5 checksum because it's quicker and if that fails we don't need to calculate the md5 checksum
Merge branch 'master' of github.com:MG-RAST/pipeline
Merge pull request #186 from jaredbischof/master

Updates and improvemets to torque file download from AWE stage
Re-wrote expanded_sims2overview so that no sorting is required previous to calling this script.  Should save on time and resources.
Merge pull request #187 from jaredbischof/master

Re-wrote expanded_sims2overview so that no sorting is required previous ...
Updated sims2annotation to produce zero-size summary files when input files are zero size.
Added handling for getting e-value exponent where e-value is zero.  Also, added source summary generation code.
Merge pull request #188 from jaredbischof/master

Updates to sims2annotation and updates to expanded_sims2overview that should make this stage parallelizable.
Added new version of sims2annotation under different name for testing in production environment before over-writing the old script version
Merge pull request #189 from jaredbischof/master

Added new version of sims2annotation under different name for testing in...