This package requires the base program TE-Greedy-Nester with which it is included to be installed first

nested-nester
nested-generator

bcbio-gff >= 0.6.4
biopython >= 1.70
click >= 6.7
networkx >= 2.1
PyYAML >= 3.12
ruamel.yaml >= 0.16.10
pyfastx >= 0.6.6
numpy >= 1.17
scipy >= 1.4.1

$ chmod +x setup.sh

# for the root privileged user 
$ sudo ./setup.sh

# or alternatively for user-space installation
$ ./setup.sh --user

Keep in mind that when installing as root, TE-Greedy-Nester needs to be installed with root privileges as well and its config.yml file needs to be located in the /etc/nested/ directory

When installing as a regular user, the config.yml file needs to be located in the ~/.local/etc/nested directory