Install stable version through PyPi

There are a few dependencies needed to get hichipper to run. All are very common bioinformatics tools / languages and should be readily available in most systems. However, note that the current implementation of hichipper is not supported on Windows platforms.

Depending on your python environment, we generally recommend using a virtual environment to keep python dependencies tidy. An example of installing hichipper inside a new python virtual environment called venv using the following sequence of commands–

virtualenv -p /usr/bin/python2.7 venv
source venv/bin/activate
pip install hichipper
hichipper --version

Install via GitHub

Though not recommended, a bleeding-edge (development) version can be installed directly from Git. Again using a virtual environment–

virtualenv -p /usr/bin/python2.7 venv
source venv/bin/active
pip3 install git+ssh://

While installing hichipper is obviously a great first step, make sure that all of the dependencies are met. Check out the next page for more detail.