How to run dockerized Rstudio server on google cloud

Dec 18, 2022 2 min read bioinformatics, docker

Create a google VM

Follow the process using the console https://cloud.google.com/compute/docs/instances/create-start-instance#console_1

Install docker

Follow https://docs.docker.com/engine/install/debian/

Note this example for the debian build. If you created your VM using ubuntu as the boot disk, you should follow the ubuntu section https://docs.docker.com/engine/install/ubuntu/.

In the GCP VM:

sudo apt-get update
sudo apt-get install \
    ca-certificates \
    curl \
    gnupg \
    lsb-release
    
sudo mkdir -p /etc/apt/keyrings
curl -fsSL https://download.docker.com/linux/debian/gpg | sudo gpg --dearmor -o /etc/apt/keyrings/docker.gpg

echo \
  "deb [arch=$(dpkg --print-architecture) signed-by=/etc/apt/keyrings/docker.gpg] https://download.docker.com/linux/debian \
  $(lsb_release -cs) stable" | sudo tee /etc/apt/sources.list.d/docker.list > /dev/null  
  
  
sudo apt-get update


sudo apt-get install docker-ce docker-ce-cli containerd.io docker-compose-plugin

verify it works

sudo docker run hello-world

Install bioconductor docker container

create a folder for R library outside the containter in your home directory on the VM.

In the GCP VM:

cd ~ 
mkdir -p R/host-site-library
cd R/host-site-library
pwd 
/home/tommytang/R/host-site-library

# make the dir writable for Rstudio to install custom R packages 
chmod a+w -R /home/tommytang/R/host-site-library

Run the docker command

 sudo docker run \
    -v /home/tommytang:/home/rstudio/tommytang \
    -v /home/tommytang/R/host-site-library:/usr/local/lib/R/host-site-library \
    -e R_LIBS_USER=/home/tommytang/R/host-site-library \
    -e PASSWORD=password \
  	-p 8787:8787 \
  	bioconductor/bioconductor_docker:RELEASE_3_15

-v /home/tommytang:/home/rstudio/tommytang mounts /home/tommytang in your VM to the docker container directory /home/rstudio/tommytang so Rstudio in the container can see your files in your VM.

-v /home/R/host-site-library:/usr/local/lib/R/host-site-library mounts /home/tommytang/R/host-site-library in your VM to the docker container directory /usr/local/lib/R/host-site-library

Note, you want to make /home/tommytang to be writable by Rstudio too.

chomd a+w -R /home/tommytang

If no password is specified, it will generated a random one in the command output.

 sudo docker run \
    -v /home/tommytang:/home/rstudio/tommytang \
    -v /home/tommytang/R/host-site-library:/usr/local/lib/R/host-site-library \
    -e R_LIBS_USER=/home/tommytang/R/host-site-library \
  	-p 8787:8787 \
  	bioconductor/bioconductor_docker:RELEASE_3_15

The first time you run this command, docker will pull the image to the VM.

ssh tunneling

execute this command in your local mac:

gcloud compute ssh tommytang@tommy-vm -- -L 8787:localhost:8787

open Rstudio server on your local computer

go to localhost:8787
type in the username: rstudio; password: <YOUR_PASS>

references

details of libpath in the docker container https://github.com/Bioconductor/bioconductor_docker/issues/10
issue I openned on github https://github.com/Bioconductor/bioconductor_docker/issues/66
https://www.bioconductor.org/help/docker/
https://github.com/Bioconductor/bioconductor_docker

bioinformatics docker