| CHSPATH | location of pipeline |
| CHSNCISPATH | path to NCIS R script (recommend: $CHSPATH/NCIS) |
| CHSBEDTOOLSPATH | path to bedtools binaries (recommend: $CHSPATH/bedtools) |
| CHSTMPPATH | temporary folder location |
| PERL5LIB | $CHSPATH must be added to the perl path |
| CHSMACSPATH | path to macs2 binary |
| PYTHONPATH | path to macs2 python libraries must be added |
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