4. python setup.py install --root=/home/user/CPAT #will install CPAT at user specified location 5. export PYTHONPATH=/home/user/CPAT/usr/local/lib/python2.7/site-packages:$PYTHONPATH. #setup PYTHONPATH 6. export PATH=/home/user/CPAT/usr/local/bin:$PATH #setup PATH Input file format FASTA file is used to represent transcript sequence or reference genome sequences. BED file is tab separated, 12 column, plain text file to represent gene model.