R in docker for the lab

This repo is to ensure reproducibility of the lab. This tutorial helped us to build and maintain this repo, many thanks.

Associated with docker images: https://hub.docker.com/r/hcp4715/rdock

About docker

Please see here for why using docker.

How to use docker images

Step 1: install docker

Linux (ubuntu): https://docs.docker.com/engine/install/ubuntu/

Windows 10: https://docs.docker.com/docker-for-windows/install/

Mac OS: https://docs.docker.com/docker-for-mac/install/

Make sure that docker was successfully installed on your machine

Step 2: pull this image form dock hub

docker pull hcp4715/rdock:sperel           # This is the image for SPEReliability project

Step 3: run the docker image

docker run -e PASSWORD=hulab1234 --cpus=4 -it --rm -p 8787:8787 -v /home/hcp4715/docker/workingDir:/home/rstudio/work hcp4715/rdock:sperel

docker run ---- Run a docker image in a container

-e PASSWORD=hulab1234 ---- set a password for rstudio, you can set your own password.

-it ---- Keep STDIN open even if not attached

--rm ---- Automatically remove the container when it exits

--cpus=4 ---- Number of cores will be used by docker. Make sure that your machine has more thread than the number here.

-v ---- Mount a folder to the container

/home/hcp4715/docker/workingDir ---- The directory of a local folder where I stored my data. [For Linux]

/d/hcp4715/docker/workingDir ---- The directory of a local folder under drive D. It appears as D:\hcp4715\docker_R in windows system.

/home/rstudio/work ---- The directory inside the docker image (the mounting point of the local folder in the docker image). Note that the docker container itself likes a mini virtual linux system, so the file system inside it is linux style.

-p ---- Publish a container’s port(s) to the host

hcp4715/rdock:sperel ---- The docker image to run. Note that you shoud include the tag :cmdstanr part, otherwise docker will instead use "hcp4715/rstudio_bayes:latest".

After running the code above, you shall see output as below:

[s6-init] making user provided files available at /var/run/s6/etc...exited 0.
[s6-init] ensuring user provided files have correct perms...exited 0.
[fix-attrs.d] applying ownership & permissions fixes...
[fix-attrs.d] done.
[cont-init.d] executing container initialization scripts...
[cont-init.d] userconf: executing... 
[cont-init.d] userconf: exited 0.
[cont-init.d] done.
[services.d] starting services
[services.d] done.
...

Step 4: Access Rstudio in browser.

Then, open your broswer (e.g., firefox, chrome), and try one of the following url in the address:

localhost:8787

http://192.168.99.100:8787

You will be asked to input username and password

Username: rstudio Password: hulab1234

Now, you will see the familiar interface of rstudio! In the broswer!

Step 4: test the iamge

Run the code below to test whether the image works

# load the libraries
library(tidyverse)

Build docker image from Dockerfile

docker build -t your_user_name/your_docker_image_name:your_tag -f Dockerfile .

Replace the your_user_name/your_docker_image_name:your_tag part with your own information. For example, I useddocker build -t hcp4715/rstudio_bayes:cmdstanr -f Dockerfile .

Final note

Docker is not perfect (yet).

hcp4715 / RDocker