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
Merge pull request #81 from ElDeveloper/emperor_conf

Add emperor configuration file
Update for biom-format 1.3.1, 1.3.1-dev

Also update QIIME to use biom-format 1.3.1.
Merge pull request #84 from jrrideout/biom-1.3.1

**NOT READY FOR MERGE!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!!1** Update for biom-format 1.3.1, 1.3.1-dev
Remove biom-format config files

These were only put in place to allow Jenkins to easily install the biom-format project. Now that biom-format is being tested using Travis (and that it is easily installable via pip), we no longer need these configs.
Merge pull request #85 from jrrideout/remove-biom

Remove biom-format config files
Remove emperor conf

Now that emperor is pip-installable and is being tested by travis-ci, we can trash this config file.
Merge pull request #86 from jrrideout/remove-emperor

Remove emperor conf
Update emperor target to 0.9.3