bbms scripts were removed from BEDOPS in the 2.x series, after adding direct support for memory usage in sort-bed through the --max-mem option
bbms.py is an equivalent implementation to bbms. bbms.py is a python script whereas bbms is a csh script. Both are provided in a small attempt to accommodate different user environment setups.
The scripts assume that the BEDOPS utilities (namely, sort-bed and bedops in this case) are in the user's PATH. It is probably best if that is true, but you can circumvent the requirement by opening whichever script you want to use and modifying (hardcoding) the calls to sort-bed and bedops to include path information.
