Parser dev

[bluegenes]

major changes:

• switch to subparsers
• addition of quality module
• manage_databases.py --> databases module
• pipeline "smart running" = only what hasn't been run/what can be run
  • if no CSV input, don't run expression
  • for other modules, check if the fasta already exists. If it does, we can pick up where the previous module left off.
• add databases to annotation, quality module. If the specified databases don't exist, download them via manage_databases, then run the task to map to that database.