Dockerfile

Here is an example of a simple Docker file. In this case, we are reusing the r-base image with tag latest; we then copy a bash script checkit.sh; and finalize with Rscript installing the igraph R package.

FROM r-base:latest
COPY checkit.sh .
RUN Rscript -e 'install.packages("igraph")'
CMD ["bash"]

Where checkit.sh has the following contents:

cd /home/docker/
R CMD check netplot

To build the docker container, named docker-example, use:

sudo docker build --compress -t docker-example .

This image is now available to be used in your computer. In case you want it to release it to https://hub.docker.com, you'd need to do the following:

sudo docker login # follow the prompts
sudo docker tag docker-example:latest uscbiostats/docker-example:latest
sudo docker push uscbiostats/docker-example:latest

Where uscbiostats is the name of the account to which you will be pushing this image. This way, users who have access to docker can simply type

sudo docker pull uscbiostats/docker-example:latest

To have access to this image that contains R with igraph installed.

Usage

To execute it interactively (with R), type:

sudo docker run -i docker-example R

Or if you want to run Rscript:

sudo docker run -i docker-example Rscript -e '1 + 1'

If you want to run it while having access to the current directory:

sudo docker run -i -v$(pwd):/home/ -w/home/ docker-example Rscript -e '1 + 1'

Running Docker in rootless-mode

https://docs.docker.com/engine/security/rootless/ while installing the rootless mode, I encountered a problem regarding a missing binary in Ubuntu 18.04. This repository had an issue with the problem:

moby/moby#41781 (comment)

In my case, I ran the following steps:

1. cd /usr/bin
2. sudo curl -o slirp4netns --fail -L https://github.com/rootless-containers/slirp4netns/releases/download/v1.1.10/slirp4netns-$(uname -m)
3. chmod +x slirp4netns