Installation

From source

Clone the repository from github

git clone https://gitlab.pasteur.fr/BaroudLab/Griottes.git

and run installation

cd Griottes
pip install .

Otherwise, a single-line option will be:

pip install git+https://gitlab.pasteur.fr/BaroudLab/Griottes.git

In order to use jupyter notebooks, you will need to install jupyter

pip install jupyterlab
jupyter lab

From Docker

Start with pulling the container

docker run -it -p 8888:8888 ghcr.io/baroudlab/griottes:latest

This will open jupyter lab in the folder with the sample notebooks (/home/jovyan/Griottes/example_notebooks) also containing paper figures.

If you want to customize starting folder, just run

docker run -it -p 8888:8888 ghcr.io/baroudlab/griottes:latest jupyter lab --notebook-dir /home/jovyan/

In order to provide your own data to the notebooks, bind your local folder as follows:

docker run -it -p 8892:8888 -v "${PWD}":/home/jovyan/work ghcr.io/baroudlab/griottes:latest jupyter lab --notebook-dir /home/jovyan/work

From Binder

Try interactive notebooks in Binder