integrativebioinformatics/sc-notebooks repository overview

⁠Installation

1. Install docker following these instructions https://docs.docker.com/install/⁠

2. Pull the latest image from DockerHub with

docker pull integrativebioinformatics/sc-notebooks

⁠Running the docker image

You can run this Docker image with the following command. Be sure to mount a local directory that contains the Cellranger index files if you plan to use them. This will also allow you to save outputs and other files outside of the Docker container.

docker run --rm -p 8888:8888 -v [local path]:/home/jovyan/work integrativebioinformatics/sc-notebooks

⁠Open Jupyter notebooks

Once the container is running, open the following URL in your browser to access the notebook:

http://127.0.0.1:8888/tree?token=SC-Notebooks⁠