To setup rDiff, please follow these steps:

1) Download the SAMTools (version 0.1.7) from http://samtools.sourceforge.net/ 
and install it. You need to add the flag -fPIC in the SAMTools Makefile for compilation.

2) Change to directory that contains rDiff and configure rDiff by typing:

./configure 

this etects and stores paths of dependencies necessary to compile and run rDiff. 
You can also set these variables manually using the interactive configuration:

./configure -i 

3) To compile rDiff, type:

make

4) When successfully completed, rDiff is usable. Check out the <Examples>:

make example

This will download an example dataset and run the rDiff.parametric on it. 
You can also run rDiff.parametric, rDiff.nonparametric or rDiff.poisson by typing:
    
make more_examples