shaleklab/scanpy-env repository overview

⁠Docker Pull

docker pull shaleklab/scanpy-env

⁠Docker Usage

Recommended use is with a docker compose file. An example is located here⁠

Simple version:

version: "3"
services:
    scanpy-env: 
        image: scanpy-env
        ports:
        - 8888:8888
        volumes:
        - .:/opt/notebooks/ 

The docker-compose.yml file should be placed in your project folder. The volumes section mounts the project folder to the opt/notebooks/ directory in the environment.

From your project folder, start the environment with

docker-compose up

Pause and unpause (stops running processes, but does not quit your session)

docker-compose pause
docker-compose unpause

Start and stop (stops running processes, quits your session, but does not remove tear down the container)

docker-compose stop
docker-compose start

Tear down container. does not delete data in the project folder

docker-compose down

⁠Use Python Notebook session locally

Open your browser and navigate to: https://localhost:8888. It will ask for a password. By default this will be jupyterlab. You can change it by giving environment variable $JUP_PW a different password hash. See example in the sample docker-compose file. To generate a new hash, type in a python/IPython shell: from notebook.auth import passwd; passwd().

See also fastgenomics/scanpy⁠, which is the prebuilt docker container Scanpy's install docs recommends and shaleklab/scanpy-env uses as its base image.