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