update README with run instructions

[andrewkern]

At this point, if the design has settled down, I think we could use some more details in the README about how to run things.

In particular we will want:

• details on the config file
• instructions on how to run Snakemake (e.g. command line examples)
• details on expected output

what else?

[xin-huang]

How to get external tools

• polyDFE: git clone https://github.com/paula-tataru/polyDFE
• DFE-alpha:
  • Download DFE-alpha: http://www.homepages.ed.ac.uk/pkeightl/dfe_alpha/download-dfe-alpha.html
  • Download DFE-alpha data tables: https://datashare.ed.ac.uk/handle/10283/2730
• grapes:
  • wget -c https://github.com/BioPP/grapes/releases/download/v1.1.0/grapes-x86_64-bin-static-1.1.0-1.tar.gz
  • tar -xvf grapes-x86_64-bin-static-1.1.0-1.tar.gz

[andrewkern]

i'm moving some of this external tool stuff into the snakemake to make install easier, and I notice that dfe-alpha requires a 5GB download!!

This isn't great. We should come up with a better way to store / serve up this file

[andrewkern]

update here: #60 has the features i mentioned above.

also i've mirrored the large file for dfe-alpha on our server at UO -- i'm hoping that will speed downloads?

[xin-huang]

I think we should let Peter Keightley know and request permission from him if we mirror the data file for dfe-alpha?

[andrewkern]

yes- good idea. let's see if it actually makes a difference in download speed first, maybe?

[andrewkern]

I believe we can close this issue when we merge #64