Merge pull request #106 from teharrison/master

fixed usage of unix sort through system()
Merge pull request #107 from teharrison/master

fix extra whitespace in system() command
Needed to add file copy from run directory back to job directory.
Merge pull request #108 from jaredbischof/master

Needed to add file copy from run directory back to job directory.
Fixed location that protein sims were being copied to after completion.
Merge pull request #109 from jaredbischof/master

Fixed location that protein sims were being copied to after completion.
Renaming "abundance" stages to "annotation" for clarity since we use the term "abundance" to describe assembly information.  Also, the term "annotation" might make more sense to the users.
Merge branch 'master' of github.com:MG-RAST/pipeline
Merge pull request #111 from jaredbischof/master

Renaming "abundance" stages to "annotation" for clarity.
Merge branch 'master' of git://github.com/MG-RAST/pipeline