Skip to content

Latest commit

 

History

History
49 lines (33 loc) · 1.91 KB

README.md

File metadata and controls

49 lines (33 loc) · 1.91 KB
Raw

sc-covarr

Single cell RNA-seq processing infrastructure

Install Docker

  1. Find your supported platform and download Docker.

Suggested instructions to install:

sudo yum update

sudo amazon-linux-extras install docker

sudo service docker start

# See https://docs.docker.com/install/linux/linux-postinstall/ to add username to a docker group to manage docker as a non-root user. Restart virtual machine to push changes and run docker run hello-world to test if command executes without sudo

sudo groupadd docker
sudo usermod -aG docker <username> 

# See https://docs.docker.com/install/linux/linux-postinstall/ to configure docker to start on boot
sudo systemctl enable docker

Run Container

This Docker container is built on rocker/tidyverse producing a debian stable work environment.

  1. To get container for the first time: docker pull kelshmo/sc-covarr
  2. Suggested configuration for running container:
docker run -d -p 8787:8787 -e PASSWORD=<insert password> kelshmo/covarr #replace <password> with your password
  • -d flag allows you the retain use of the terminal while the Docker image is running
  • -p specifies port of choice
  • -e designates a password to login to RStudio

If you are having trouble with your Docker, this documentation (or this documentation) may be useful.

  1. Now, RStudio has launched invisibly. Open a browser and enter your ip address followed by :8787. You should be greeted by the RStudio welcome screen.
username: rstudio
password: <password>
  1. You can docker stop <container name> to pause your work and return to it later with docker start <container name>.
  • To find your container name docker ps -a