Docker: keep your secrets secret


Josiah Parry


June 11, 2024

You’ve written a shiny app, plumber API, or an ETL process. Your orchestrating that work with Docker. In order for the application to work, you need to be able to use secret values.

How can you use secrets with a Docker image safely?

Example Dockerfile

Here is a very simple Dockerfile. Say the container is called supersecret. When we run the Docker container we print a single environment variable.

FROM rhub/r-minimal

CMD [ "R", "--slave", "-e", "cat(Sys.getenv('SECRET_USER'))"]

Run this with docker run --rm -t supersecret and you’ll see nothing printed to the console. This is because the environment variable is not actually available to the container.

How can you set the environment variables used by a container?

The ENV instruction

The ENV Docker instruction is used to specify environment variables You can specify environment variables directly into the Dockerfile like so:

FROM rhub/r-minimal

CMD [ "R", "--slave", "-e", "cat(Sys.getenv('SECRET_USER'))"]

Running docker run --rm -t supersecret will print josiah to the console! So that worked.

This is fine for things that dont need to be secret. For example maybe you have something like ENV DEBUG=true to specify that this is a debug build.

But if you have a secret, you shouldn’t place your secrets directly in the code of the Dockerfile.

Using --env

Another way to specify environment variables is to specify the environment variables at run time using the --env flag. This accepts key-value pairs for the environment variables.

For example

docker run --env SECRET_USER="ricky bobby" --rm -t supersecret

will print ricky bobby to the console.

This will work but it requires that you manually specify the environment variables at run time when using docker run. And that can be cumbersome and require some finagling.

And again, you dont want to write a bash script that hard codes those values into a docker run call.

So what else can you do?

Using a separate file with --env-file

You shouldn’t store secrets in your R code. You should use a .Renviron file. This looks like


In many other languages and ecosystem, using a .env file with the same structure is used to set environment variables.

This would make the environment variables KEY, SECRET_USER and SECRET_USER_PASSWORD available to your R session by running Sys.getenv().

Now, you don’t want to actually copy this file into the docker container. What if you accidentally made the file available? Yikes!

Instead, you can pass the file directly using the --env-file flag. This will capture the environment variables written in a file as a KEY=value pair and make them available in your container.

docker run with file

Given the following files which define a Docker image called supersecret

FROM rhub/r-minimal

CMD [ "R", "--slave", "-e", "cat(Sys.getenv('SECRET_USER'))"]

You will need to run docker run --env-file .env supersecret to set your environment variables appropriately.