Renaming 2 files from the annotation stage so they fit into the current job directory structure.
Merge pull request #172 from jaredbischof/master

Renaming 2 files from the annotation stage so they fit into the current job directory structure.
Typo.
Merge pull request #173 from jaredbischof/master

Typo
Edited new loadDB stage to add both sims and annotation versions into jobs database.
Merge pull request #174 from jaredbischof/master

Edited new loadDB stage to add both sims and annotation versions into jobs database.
Merge pull request #175 from wtangiit/master

make sure job number in awe_annotate.pl is integer
Removed code that enters default filtering options when none are specified because these options will be set explicitly at job submission and also we need the ability to run this stage with no filtering options which the current configuration would not allow.
Merge pull request #176 from jaredbischof/master

Allowing awe_preprocess.pl to be run with no filtering options without enforcing any default filtering setting.
Script should not die if one job is not complete.
Added check for running instance of cron script so that this script will die if another instance is already running.  Also, added code to update job statuses in JobDB based on AWE status.  Need to update mgrast awe template so that mgrast stage names mostly match awe process descriptions.
Edited the mgrast awe template to have process descriptions the same as the mgrast stage names when possible for updating job statuses.
Some edits to update mgrast stage statuses roughly following the AWE process states.
Merge pull request #177 from jaredbischof/master

More edits to script that will submit the remainder of the MG-RAST jobs that have run thru AWE and the MGRAST AWE pipeline template.
add refdb urls in job template (for refdb downloading at runtime)
Merge branch 'master' of github.com:wtangiit/pipeline