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.

3. 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>

4. 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