BuildABiocWorkshop

This package is a template for building a Bioconductor workshop. The package includes Github actions to:

  1. Set up bioconductor/bioconductor_docker:devel on Github resources
  2. Install package dependencies for your package (based on the DESCRIPTION file)
  3. Run rcmdcheck::rcmdcheck
  4. Build a pkgdown website and push it to github pages
  5. Build a docker image with the installed package and dependencies and deploy to the Github Container Repository at the name ghcr.io/gihub_user/repo_name, all lowercase.

Responsibilities

Package authors are primarily responsible for:

  1. Creating a landing site of their choosing for their workshops (a website). This website should be listed in the DESCRIPTION file as the URL.
  2. Creating a docker image that will contain workshop materials and the installed packages necessary to run those materials. The name of the resulting docker image, including “tag” if desired, should be listed in a non-standard tag, DockerImage: in the DESCRIPTION file.

Both of those tasks can be accomplished using the Github actions included in this template package. The vignette accompanying this package describes how to accomplish both of these tasks.

Details

For detailed instructions, see the How to build a workshop article/vignette.

Results of successful deployment

  • A working docker image that contains the installed package and dependencies.
  • An up-to-date pkgdown website at https://YOURUSERNAME.github.io/YOURREPOSITORYNAME/
  • Docker image will be tagged with latest, sha-XXXXXX where XXXXXX is the hash of the current master commit, and master.

To use the resulting image: 

docker run -e PASSWORD=<choose_a_password_for_rstudio> -p 8787:8787 YOURDOCKERIMAGENAME

Once running, navigate to http://localhost:8787/ and then login with rstudio:yourchosenpassword.

To try with this repository docker image:

docker run -e PASSWORD=abc -p 8787:8787 ghcr.io/bioconductor/buildabiocworkshop

NOTE: Running docker that uses the password in plain text like above exposes the password to others in a multi-user system (like a shared workstation or compute node). In practice, consider using an environment variable instead of plain text to pass along passwords and other secrets in docker command lines.

Alternative: connect from Positron over SSH

This repository also includes Dockerfile.positron, which keeps the Bioconductor base image and package installation steps but starts an SSH server instead of RStudio Server. Build it explicitly with:

docker build -f Dockerfile.positron -t buildabiocworkshop-positron .
export PASSWORD='choose-a-password'
docker run --rm --env PASSWORD -p 2222:22 buildabiocworkshop-positron

Then connect to ssh://rstudio@localhost:2222 from a local Positron install using the same password you supplied in PASSWORD.

Whatcha get