LSHTM_analysis/README.md

mCSM

This contains scripts that does the following:

1. mcsm.py: function for submitting mcsm job and extracting results
2. run_mcsm.py: wrapper to call mcsm.py

foldx

This contains scripts that does the following:

1. runFoldx.py: submitting foldx requests and extracting results
2. runfoldx.sh: is wrapped by runFoldx.py

Requires an additional 'Data' directory. Batteries not included:-)

Assumptions

1. git repos are cloned to ~/git
2. Requires a data directory with an input and output subdirs. Can be specified on the CLI with --datadir, and optionally can be created with mk_drug_dirs.sh <DRUG_NAME>

LSHTM_analysis:

subdirs within this repo

 scripts
 	*.R
 	*.py
	plotting/
	*.R
 mcsm
	*.py
 foldx
 	*.py
	*.sh
  

More docs here as I write them.