How To Build A Workshop Package

In other words, how do I use what’s here

Sean Davis1

Source: vignettes/HOWTO_BUILD_WORKSHOP.Rmd

First, this package doesn’t do much except add a template Github Action to build all the pieces necessary for a workshop.

Quickstart

  • Clone this repo, fork and rename it, or create a repo from this template
  • Edit DESCRIPTION file
    • Change package name
    • Change title and description
    • Change authors
    • Check dependencies
    • Change DockerImage tag
  • Edit .github/workflows/basic_checks.yaml
  • Write a normal R package that can be installed
  • Include one or more vignettes that will constitute the workshop materials

Details

Clone this repo

git clone https://github.com/seandavi/BuildABiocWorkshop2020 MYPKGDIR

Edit DESCRIPTION file

  • Change the package name to something identifiable and descriptive, ideally something that will be somewhat unique.
  • Edit the title and description as per any normal R package.
  • Update authors (unless you want me to get credit for your work).
  • Workshop packages are normal R packages, so dependencies work as usual. If you are going to depend on something on github, be sure to specify the correct repo username/reponame. Installation will deal with this.

Edit .github/workflows/basic_checks.yaml

You MUST change the repository line in this yaml file to be YOUR desired Docker image name. In other words, this section of the github actions file will build and push to dockerhub the image with this name.

     - uses: docker/build-push-action@v1
        with:
          username: ${{ secrets.DOCKER_USERNAME }}
          password: ${{ secrets.DOCKER_PASSWORD }}
          # change the next line to reflect the name
          # of YOUR dockerhub repository
          repository: seandavi/buildabiocworkshop2020
          tag_with_ref: true
          tag_with_sha: true
          tags: latest

Add “secrets” to github repo

Secrets are encrypted environment variables that you create in a repository or organization. The secrets you create are available to use in GitHub Actions workflows. GitHub uses a libsodium sealed box to help ensure that secrets are encrypted before they reach GitHub, and remain encrypted until you use them in a workflow.

See Creating and storing encrypted secrets

  • DOCKER_USERNAME: your dockerhub username; create a dockerhub account if you do not have one
  • DOCKER_PASSWORD: your dockerhub password or an access token obtained from Docker Hub

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