Merge pull request #111 from jaredbischof/master

Renaming "abundance" stages to "annotation" for clarity.
fix fix stage
Merge branch 'master' of git://github.com/MG-RAST/pipeline
Merge pull request #112 from teharrison/master

fix fix stage
Merge pull request #113 from jaredbischof/master

No longer using a separate pipeline configuration for this script.
Merge pull request #114 from jaredbischof/master

Fixed script name in usage message.
Merge pull request #115 from jaredbischof/master

Added sort memory as an option and passed that to sims2annotation script.
Merge pull request #116 from jaredbischof/master

Fixed printed script options.
Merge pull request #117 from jaredbischof/master

Fixed filename.
add awe wrapper for sims2annotation
Merge pull request #119 from jaredbischof/master

Removing files from list of required output files that are no longer going to be generated by pipeline.
Merge pull request #120 from jaredbischof/master

Changing some pipeline file names.
Merge pull request #121 from jaredbischof/master

Adding a couple filename variables.
Merge pull request #122 from jaredbischof/master

More edits for modified pipeline with annotation stage.
awe_cluster_parallel.pl update for keeping map files
added stripping of html tags from inputted metadata
Merge pull request #123 from teharrison/master

added stripping of html tags from inputted metadata
Merge pull request #118 from wtangiit/master

awe wrappers addition and updates
fix in awe_cluster_parallel.pl
Merge pull request #124 from wtangiit/master

Fix for pull request #118