Checks md5 regardless of need to download; listener gets only RECEIVED status submissions.
Improved reference handling.
Added functions for md5, locate ref, getBAM.
Writes out commands to file and includes in provenance.
Adds evaluation to prov for commands file.
Calls functions from seq_running, one activity for two outputs, still needs index.
Added function to copy ref from head to worker.
Gets index.
Updated scripts list and dependency list.
Fixed dependency list.
Functions for importing external data.
Added use of AWS CLI for getting private data.
Added boto to deps.
Added main().
Added sailfish and featurecounts.
Now parseJobParams doesn't overwrite bucket annotations.
Unzips-tars reference index on local.
Added TODO for loading external.
Get submission rather than entity, changes status to closed.