Linux, Windows and Mac OS are supported for running the code. At least 8 GB of RAM is required to run the software. 32GB may be required for larger images. The software has been heavily tested on Ubuntu 22.04 and less-tested on Mac OS and Windows 10. Please open an issue if you have any problems with installation.
This install a cross-platform, pure python version of CellMet. Some advanced features are not available, namely:
pip install CellMetThose are the instructions to install the package from source on a debian-like linux distribution. If you already have a basic scientific python stack, use it, don't install anaconda.
If you want to do that, I assume you already know how to manage
dependencies on your platform. The simplest way to manage dependencies is to use conda to manage the dependencies (you can use mamba as a faster alternative to conda).
git clone --recursive https://github.com/TimSaundersLab/CellMet.git
cd CellMetThen create a virtual environment:
conda create --name cellmetThen install python:
pip install .
If all went well, you have successfully installed CellMet.