[EGGO-18] WIP: Setup config files

[laserson]

@tomwhite, could you check this out. I want to get your opinion before I keep going in this direction. I haven't tested any of it yet, so there are for-sure many random bugs to clean up.

[laserson]

Mainly, I add a config file for eggo and try to get as many options from there as possible. There is still opportunity for quite a bit more. Now, the user should generally only need to specify an EGGO_CONFIG variable pointing to their configuration. Hopefully this'll make it easy to keep test profiles as well, for running locally and against HDFS and S3.

[laserson]

Ok, this is quite a large set of changes. Apologies @tomwhite. Also note to use the eggo command instead of fab. And you must also run a deploy_eggo_config command in there as well. This needs serious cleanup, but should now be able to be broken down into digestible tasks. CI is definitely needed...

[tomwhite]

Sorry I haven't had time to look at this. We should probably test changes before merging substantial updates like this. +1 to the direction though.

Nit: we could default EGGO_HOME and EGGO_CONFIG quite easily relative to bin/eggo.

[laserson]

Yeah, I agree, but figured I'd let this one go bc eggo is still rather unstable anyway. Also, I was (basically) able to get the test-genotypes pipeline running with all these changes.

[tomwhite]

That's good to hear. We do need a functional test that we can run under CI (#46) - I'll see if I can tackle it next week.

This change also means the outstanding PRs (#52, #38) need to be essentially re-written :(