Environmental variables in Rocker

How to use environmental variables to pass values to a R docker

Introduction

The idea of having R docker able to get external values when running is quite interesting.

As an example, suppose you have a docker that performs x+1 and that you want to pass x to the docker when running it.

The easiest way consist of forcing R to read x from an environmental variable, say X and then pass X to the docker with the --env option.

Docker File

Suppose you have a R docker build by the following dockerfile:

FROM rocker/r-ver:4.0.5

RUN mkdir /data
 
RUN mkdir /app
RUN chmod -R 755 /app

WORKDIR /app
ADD main.R .
CMD R -e  "source('main.R')"

Main R script

Where the script main.R is:

x <- Sys.getenv("X")
y <- x+1
write(y, '/data/y.txt')

Run

After building the docker with:

docker build -t mydocker .

You can run it with

sudo docker run --env X=99 --rm -v /data/:/data  mydocker

You should see the value of y, presumably 100, in the output file y.txt