Add reference files to database after download

Fixes #392
rename qiita_ware run.py
add new processing function and add to handler. Fix #420
Fix #421 and Fix #419
Merge branch 'master' of https://github.com/biocore/qiita into add_ref_to_db-issue-392

Conflicts:
	qiita_db/environment_manager.py
rename test file
Fix #424
remove init on RunAnalysis
Merge pull request #422 from antgonza/issue_421

Fix #421 and Fix #419
Merge pull request #426 from antgonza/issue_424

Fix #424
Merge pull request #395 from adamrp/add_ref_to_db-issue-392

Add reference files to database after download
Merge pull request #428 from squirrelo/issue-420

Issue 420
Solving merge conflicts and addressing comments