djproc/scanpy-spatial repository overview

This image is based on the jupyter datascience:latest image (2021-01-19) with additional packages to get Scanpy running.

⁠COMMAND FOR LINUX/MAC/WSL2:

docker run --rm -p 9898:8888 --user root -e JUPYTER_ENABLE_LAB=yes -e GRANT_SUDO=yes -v "$PWD":/home/jovyan/work djproc/scanpy-spatial:v001a

This command will run Jupyter Lab (with Python, R, or Julia kernels) which is accessible from your browser by entering "localhost:9898" into the address bar. You will have to enter the token found at the end of the path displayed in the terminal when the container starts running. The container will be able to access any files below the current working directory of your terminal (I usually choose the home/user folder) via the file browser of Jupyter Lab. All these files will be under a folder called "work". This will also give the user admin privileges at root.

⁠COMMAND FOR WINDOWS 10 cmd:

docker run --rm -p 9898:8888 --user root -e JUPYTER_ENABLE_LAB=yes -e GRANT_SUDO=yes -v %CD%:/home/jovyan/work djproc/scanpy-spatial:v001a

This command will run Jupyter Lab (with Python, R, or Julia kernels) which is accessible from your browser by entering "localhost:9898" into the address bar. You will have to enter the token found at the end of the path displayed in the terminal when the container starts running. The container will be able to access any files below the current working directory of your terminal (I usually choose the home/user folder) via the file browser of Jupyter Lab. All these files will be under a folder called "work". This will also give the user admin privileges at root.