prete/seurat-studio repository overview

⁠Jupyter Notebook + RStudio

Base container for people who need jupyter notebook and RStudio in the same image.

⁠Main stack

(based on base-notebook⁠)

• Jupyer Notebook
• RStudio Server 1.5.9.923
• R (3.6.2)

⁠Python libraries

• scipy
• scanpy
• python-igraph
• louvain
• bbknn
• rpy2
• leidenalg
• pandas

⁠Run

docker run --name jovyan-studio --detach --publish 80:8888 --env GRANT_SUDO=yes --user root --volume ${PWD}:/home/jovyan prete/jupyter-rstudio:3.2.6

To get the token for log in in use docker logs jovyan-studio and it will show the output of the jupyter launch command that is used to start the notebook.

⁠Jupyter notebook config file

Create a new jupyter configuration file and place it inside {VOLUME_PATH}/.jupyter/jupyter_notebook_config.py For quick and UNSECURE access you can set c.NotebookApp.token = ''. Read more about securing a notebook server⁠ on the official documentation.

⁠Disclaimer

There are probably a whole bunch of python libraries or system packages that you don't really need (fuse/sshfs/openjdk) but they make my life easier.