...
Make a lib directory unless this already exists:
mkdir lib
Lone Clone this into the lib folder you just make using git:
git clone https://github.com/swo/smile_trainalmlab/SmileTrain
To get some information, you have to have this documentation for each any time this code is modified (i.e. below, this is ok for 5/12/14), you need to have sphinx-build, which isn't in on coyote. If you can't generate this, don't give up, just email Scott (swo@mit.edu).
(open the html file within the _build folder on the Desktop to get really good documentation)
go to the wiki and follow the directions:
https://github.com/almlab/SmileTrain/wiki
Alter train.cfg (you either have to link to usearch etc) to have your new names for the following (for example I changed these):
...
library=/net/radiodurans/alm/spacocha/lib/smile_trainSmileTrain
bashrc=/net/radiodurans/alm/spacocha/lib/smile_trainSmileTrain/bashrcs/coyote.sh
Then, make the tmp_directory:
...