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Installation

Prerequisites

CHESS was written and tested using Python 3.6 - 3.8.2 on Scientific Linux (6.10) and OS X El Capitan (10.11.6) and Ubuntu Bionic Beaver (18.04) and Ubuntu Focal Fossa (20.04).

It requires the packages cython (0.29.16), scipy (1.0.0), numpy (1.14.0), scikit-image (0.13.1), pandas (0.22.0), pathos (0.2.1), kneed (0.6.0), tqdm (4.43.0), intervaltree (3.0.2), pybedtools (0.8.1), future (0.16.0) and fanc (0.8.28).

When installing with a python version < 3.8.2, Please make sure to have `cython` (0.29.16) installed before installling CHESS via `pip` or `python install setup.py`, or use a `pip` version >= 20.0.2.

Installation from the Python Package Index (PyPi)

CHESS can be installed quickly from the command line using PyPi:

pip install chess-hic

Installation from source

You can also download the code from our GitHub repo and install CHESS manually. Make sure to have cython installed. The other dependencies should be downloaded autmatically; if you encounter problems, try to install the other :ref:`prerequisites <prerequisites>` manually.

git clone https://github.com/vaquerizaslab/chess  # or download manually
cd chess
pip install .