shaleklab/seurat-env repository overview

⁠Seurat in Docker

⁠Docker Pull

docker pull shaleklab/seurat-env

⁠Docker Usage

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

Simple version:

version: "3"
services:
    rstudio: 
        image: shaleklab/seurat-env
        ports:
        - 8787:8787
        volumes:
        - .:/home/rstudio/   

The docker-compose.yml file should be placed in your project folder. The volumes section mounts the project folder to rstudios working 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 R session locally

Open your browser and navigate to: https://localhost:8787

You will find a login screen. default username and password are rstudio and rstudio.

See the rocker website⁠ for more info.