Popular Computational Biology Language with R - [Proj:My Computer Workbench]

Introduction

For this part of My Computer Workbench, I would like to explain the programming language I am using. Additionally, this section covers trick for R and how to use R with reproducibility in mind.

R and R studio

I mostly use R and Rstudio mostly for my downstream analysis and visualization. However, I have encountered program dependency problems when running R on Linux. As a solution, I have started using dockerized RStudio to create an RStudio server.

Here is the code for running dockerized RStudio.

Step 1 Create directory for the Dockerized R studio

cd /home/namthip
mkdir R
cd R
mkdir host-site-library

Step 2 Give writable permission on `host-site-library`, to install custom R packages

chmod a+w -R /home/namthip/R/host-site-library

Step 3 To initialize the Dockerized R Studio and open RStudio Server

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

I pull a Docker image from bioconductor (as suggested by Tommy in his blog post). I think this Docker image is great. They explain clearly how to mount a volume (directory). I had tried other Docker images and found that some cannot mount the volume, while others cannot install new packages. This is my own RStudio server on my computer.

R Studio server opened on my computer

Please note that the path that you use in the dockerized R is the path in the container, otherwise dockerized R can’t find your destination. You can easily find the path by using Terminal in the dockerized R studio. Going to the directory you want, then use pwd command to find the path of that directory.

Trick

1. R version

One big problem I found with R version issues is the compatibility between the R version and package version. Sometimes we need a newer version, but sometimes the old one works fine. To switch between R versions, I use this trick.

Docker allows us to pull a specific version of a docker image, as shown in the picture (or this link.)

Different version of R on Docker Hub

The version of R will be shown in the docker file for each version. From the picture below, “R version 4.4.1” is stated on line number 7.

Docker file of R version 4.4.1

From this point, I pull “R version 4.4.1” from docker, mount the same volume, and initialize a Dockerized R Studio and open RStudio Server using the command line below.

 sudo docker run \
    -v /home/namthip:/home/rstudio/namthip \
    -v /home/namthip/R/host-site-library:/usr/local/lib/R/host-site-library \
    -e R_LIBS_USER=/home/namthip/R/host-site-library \
    -e PASSWORD=<MY_PASSWORD> \
  	-p 8787:8787 \
  	bioconductor/bioconductor_docker:RELEASE_3_19-R-4.4.1

After launching the container, we need to access RStudio Server by opening an internet browser and typing localhost:8787. The login page for RStudio Server will appear. The username will always be rstudio and the password is the one you defined.

2. Best practice for R

If you start using R, it is good to do so following this suggestion “Best Practice for R”. I started using R quite from scratch; I had to fix so many things afterward.

Cheast sheet: Best Practice for R

3. Run Dockerized Rstudio server using 1 line command with Docker Compose

I found a easier way to use R studio server in Docker. Previously, I have used very long command shown above in Step 3

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

Instead of this, we will use one command line docker compose up -d.

Step 1: Prepare docker-compose.yml file

However, before that easy step, we have to prepare docker-compose.yml file first. Use information below, save, and named it exactly this docker-compose.yml file.

version: "3.8"
services:
  rstudio:
    image: bioconductor/bioconductor_docker:RELEASE_3_15
    ports:
      - "8787:8787"
    volumes:
      - /home/namthip:/home/rstudio/namthip
      - /home/namthip/R/host-site-library:/usr/local/lib/R/host-site-library
    environment:
      - R_LIBS_USER=/home/namthip/R/host-site-library
      - PASSWORD=<MY_PASSWORD>

Step 2: Open R studio server

Go to directory you store docker-compose.yml
Type this to start the container.
```
sudo docker compose up -d
```
Here, we already open Rstudio server in port 8787.
I can use Rstudio server by opening an internet browser and typing localhost:8787.
After finish using it, go to the directory you store docker-compose.yml again.
Then stop docker container by typing.
```
sudo docker compose down
```
Note: Don’t forget turn it off before close your computer.