Installation

Prerequisites

Cassiopeia currently requires python version 3.10 and above, which are publicly available.

Installing

For basic users, you can download Cassiopeia via pip as so:

::

pip install git+https://github.com/YosefLab/Cassiopeia@master#egg=cassiopeia-lineage

To run some of the models in Cassiopeia, you will also need to install Gurobi. Licenses are free to academic users and can be downloaded here.

For developers, you can clone the code from Github as so:

git clone https://github.com/YosefLab/Cassiopeia.git

Once Cassiopeia is cloned into a directory onto your machine, enter into the directory with cd Cassiopeia. To make installation simple, we have wrapped the installation steps into a MAKEFILE - this allows you to install Cassiopeia with the command:

make install

To make sure that the package has been installed correctly, we recommend you also run all the unit tests with another command from the MAKEFILE:

make test