Use Luigi?

[averagehat]

Luigi might make it easier to handle making overall pipeline changes like
#110 or #150

Also will allow automatic checkpointing, diagram construction, and allows stages to be run in chunks/independently.

Edit: An initial implementation might just be to wrap each script call in runsample.py in a luigi task.
Related: http://ratatosk.readthedocs.org/en/latest/dev/introduction.html

[averagehat]

Closing in favor of #155, as Luigi requires a running Tornado server and is more verbose. If we hit the limits of Make we can consider it among some other options.