workshop-r

This repo contains the course material for NBIS workshop R Programming Foundation for Life Scientists. The rendered view of this repo is available here.

Contributing

To add or update contents of this repo (for collaborators), first clone the repo.

git clone https://github.com/nbisweden/workshop-r.git

Make changes/updates as needed. Add the changed files. Commit it. Then push the repo back.

git add .
git commit -m "I did this and that"
git push origin

If you are not added as a collaborator, first fork this repo to your account, then clone it locally, make changes, commit, push to your repo, then submit a pull request to this repo.

❗ When updating repo for a new course, change output_dir: XXXX in _site.yml as the first thing, so that old rendered files are not overwritten.

❗ Do not push any rendered .html files or intermediates.

Repo organisation

The source material is located on the master branch (default). The rendered material is located on the gh-pages branch. For most part, one only needs to update content in master. Changes pushed to the master branch is automatically rendered to the gh-pages branch.

For more details about repo organisation, updating and modifying this repo, check out the template repo.

Schedule

Schedule is saved into the schedule.csv file. It is a csv file with semi-colon as delimiter. You should NOT try to edit it in a text editor, but use proper spreadsheet. If you are using command line, you can install vd and open and edit the file vd --csv-delimiter ';' schedule.csv.

Docker

R packages needed to build the website and run the labs are all contained in a Docker container. To run docker container locally, follow instructions below:

❗ Image is about 4.8 GB!

# pull the container
docker pull --platform=linux/amd64 ghcr.io/nbisweden/workshop-r:latest

# render whole website
docker run --platform=linux/amd64 --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-r:latest Rscript -e 'rmarkdown::render_site()'

# render one file
docker run --platform=linux/amd64 --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-r:latest Rscript -e 'rmarkdown::render("index.Rmd")'

To run RStudio server and develop in the browser, run;

docker run --platform=linux/amd64 --rm -e PASSWORD=rstudio -p 8788:8787 -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-r:latest

Go to http://localhost:8788/ or http://0.0.0.0:8788. Username is rstudio and password is rstudio. Change to folder /rmd to see your files.

To add new packages, you need to update Dockerfile, rebuild the container, test it and push it to repository. Make changes to the Dockerfile as needed. Then to rebuild and push the docker image, follow the steps below:

❗ Remember to update the version number ❗ Remember to render the whole website to make sure everything works

# build container and add tags
docker build --platform=linux/amd64 -t ghcr.io/nbisweden/workshop-r:1.1.2 .
docker tag ghcr.io/nbisweden/workshop-r:1.1.2 ghcr.io/nbisweden/workshop-r:latest

# push to ghcr
docker login ghcr.io
docker push ghcr.io/nbisweden/workshop-r:1.1.2
docker push ghcr.io/nbisweden/workshop-r:latest

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2024 NBIS • SciLifeLab