Merge pull request #336 from wgerlach/master

added docker images and BASH_ENV
update resubmit to remove old awe job
Merge pull request #337 from teharrison/master

update resubmit to remove old awe job
update resubmit to remove old awe job
Merge pull request #338 from teharrison/master

update resubmit to remove old awe job
fix fiule pathing
Merge pull request #339 from teharrison/master

fix file pathing
bug fix
bug fix
fix perl warnings
Merge pull request #340 from teharrison/master

minor bug fixes
Merge branch 'master' of github.com:MG-RAST/pipeline