update rtax to 0.984
Merge pull request #74 from davidsoergel/master

update rtax to 0.984
updated pynast version
Merge pull request #76 from gregcaporaso/pynast-1.2.1

updated pynast version
Fix pynast 1.2.1 filename
Merge pull request #77 from jrrideout/master

Fix pynast 1.2.1 filename
Updates versions of NumPy and R
Merge pull request #78 from samfway/update_deps

Update versions of NumPy and R
added paired end assembler apps
Merge pull request #79 from gregcaporaso/paired-end-assemblers

added paired end assembler apps
Fix seqprep target
Merge pull request #80 from jrrideout/master

Fix seqprep target
Add emperor configuration file

This configuration file supports an installation of Emperor only. This
should be useful to deploy in the Jenkins-CI server.
Remove the setup tools
Change directory name
Remove extraneous README.md files

Also update biom-format 1.2.0-dev to depend on pyqi 0.3.1.
Merge pull request #82 from jrrideout/master

Remove extraneous README.md files
Add setuptools target to biom-format conf
Merge pull request #83 from jrrideout/master

Add setuptools target to biom-format conf
Add setuptools to the configuration file