To install the tool, you will first have to cp chilin.conf to chilin.conf.filled and modify chilin.conf to define site-wide defaults for your system.
In chilin.conf, there are three main sections-- tools, references, and params.
In the tools section, you will have to define the absolute paths to the various sub-tools or modules in the analysis pipeline.
In the references section, you will have to define the absolute paths to the reference files (e.g. assembly, DHS file, gene regions, etc.) for the species you wish to support. Please read 'Generating Species References' below for information on how to generate files for your species of interest.
In the params section, you will have the ability to fine-tune and define site-wide defaults for some of the sub-tools/modules. NOTE: the defaults should work for almost all installations--only make modifications only if you are sure!
After tailoring chilin.conf to suit your system's needs, simple type: python setup.py install
NOTE: if you are installing system-wide, you may want to add 'sudo' in front of that command
Finally, don't forget to add your species to chilin.conf.
cistrome chilin document: http://cistrome.org/chilin