For Debian, cnrun is configured --with-tools=no.  These tools are:

 - varfold, a matrix convolution utility;

 - hh-latency-estimator, for measurement of first-spike latency
   in response to stimulation, and

 - spike2sdf, for estimation of a spike density function from a record of
   spike times.

These utilities were used in the original experiment
(http://johnhommer.com/academic/code/cnrun/ratiocoding), and hence not
deemed of general purpose enough to be included in the Debian package.
If you believe you have a particular need for any of them, feel free
to build cnrun from source.