install.rst

Installation

The OpenMiChroM library can be installed via conda or pip, or compiled from source (GitHub).

Install via conda

The code below will install OpenMiChroM from conda-forge.

conda install -c conda-forge OpenMiChroM

Hint

Often, the installation via conda happens to be stuck. If this is the case, it is recommended to update conda/anaconda using the command line below and try to install OpenMiChroM again.

conda update --prefix /path/to/anaconda3/ anaconda

Install via pip

The code below will install OpenMiChroM from PyPI.

pip3 install OpenMiChroM

Note

The OpenMiChroM library uses OpenMM API to run the chromatin dynamics simulations. These requirements can be met by installing the OpenMM package from the conda-forge channel:

conda install -c conda-forge openmm

The following are libraries required for installing OpenMiChroM:

• Python (>=3.6)
• NumPy (>=1.14)
• SciPy (>=1.5.0)
• six (>=1.14.0)
• h5py (>=2.0.0)
• pandas (>=1.0.0)
• scikit-learn (>=0.20.0)