Docker is an incredibly useful tool for running reproducible analysis workflows. For
useRs, the rocker collection of images is very convenient for creating version-controlled R environments. This is pretty straightforward if you are using packages on CRAN, or publicly available packages on GitHub. But what if we want to use private packages on GitHub, or need for any other reason to enter authentication credentials during the build?
There are various ways to copy data into the image during the build, but when handling secrets that we don’t want hanging around after it’s finished, caution is needed. Approaches such as using
ARGS will leave traces in the build. Staged builds are more secure, but tricky. Fortunately, as of v. 18.09, Docker is now providing official support for handling secrets.
A simple example
Here is how to use the new Docker features to securely pass a secret during a build 1.
There are few non-default settings that need to be specified for this. First of all, prior to the
docker build command, you need to specify that you want to use the new BuildKit backend with
DOCKER_BUILDKIT=1. So the command starts
DOCKER_BUILDKIT=1 docker build ...
Next, we must add a syntax directive to the top line of the
Dockerfile. For example, for a
Dockerfile based on
# syntax=docker/dockerfile:1.0.0-experimental FROM rocker/tidyverse
echo "FABULOUS" > my_secret_stash
This is all we need to use secrets during the build. Here is an example
Dockerfile similar to the one in the Docker documentation.
# syntax = docker/dockerfile:1.0-experimental FROM alpine RUN --mount=type=secret,id=mysecret cat /run/secrets/mysecret
To see how it works, save this as
Dockerfile, then from the same directory containing
my_secret_stash, build the image:
DOCKER_BUILDKIT=1 docker build --progress=plain --no-cache --secret id=mysecret,src=my_secret_stash .
I’ve truncated the output, but at build step #7 you should see something like this.
Can you spot our secret? It’s showing up from the
cat command. However, it will not remain in the image.
Installing a private R package
To install a package from my private GitHub repo, I created an additional simple R script, called
secret <- commandArgs(trailing = TRUE) devtools::install_github("joelnitta/my-private-package", auth_token = secret)
commandArgs(trailing = TRUE) will return whatever command line arguments were passed to
Rscript after the name of the script, as a character vector.
We will call this script from the
Dockerfile and pass the secret to it.
Here is the Dockerfile to do that. (Note that although we copy the
install_git_packages.R script into the image, we are passing it the secret variable that is only present during the build, so this should not remain afterwards.)
# syntax = docker/dockerfile:1.0-experimental FROM rocker/tidyverse:3.5.1 ENV DEBIAN_FRONTEND noninteractive COPY install_git_packages.R . RUN apt-get update RUN --mount=type=secret,id=mysecret \ Rscript install_git_packages.R `cat /run/secrets/mysecret`
Let’s build the image and tag it:
DOCKER_BUILDKIT=1 docker build --progress=plain --no-cache --secret id=mysecret,src=my_secret_stash . -t my_special_image