INSTALL

This is GREMLIN v2.01 - a version that learns a Markov Random Field from an input alignment with parameters optimized for accuracy and speed of contact prediction.

You have two options to run gremlin code

1) As a matlab function:

  a) compile the mex executables for your system architecture as follows:

  within matlab, go to the gremlin dir and type

  >mexAll

  b) add gremlin to your matlabpath. One way to do this is to go to the gremlin src dir in matlab and then type

  >addpath(genpath(pwd));

or,

2) As a compiled executable:

You'll need to compile on a m/c that has a matlab license (with the statistics toolbox) which has the same architecture as the machine  you plan
to run on. If you are running on a linux x86-64 machine, you might be able to use the precompiled executables bundled
with this tar-ball. You'll also need the matlab component runtime (MCR) installed on the machine you run the code on
(this can be freely downloaded from the mathworks website without having a MATLAB license).

To compile:
go to the gremlin directory 
type on the unix shell (expects mcc to be on your path)
$bash make.sh

This should create an executable called gremlin end an wrapper shell script called run_gremlin.sh

You may use run_gremlin.sh just as you call gremlin but with one additional parameter at the beginning: the path to the MCR

Note:
This version of gremlin uses pdist which is included with the statistics toolkit. 
We are working on a providing an alternate which does not need this toolkit.