This repo contains the material for NBIS workshop Analysis of RNA-Seq data. The rendered view of this repo is available here.
To add or update contents of this repo (for collaborators), first clone the repo.
git clone https://github.com/nbisweden/workshop-RNAseq.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.
You can preview changes and build the whole website locally without a local installation of R or dependency packages by using the pre-built Docker image.
❗ Note: Large image size: 4.6GB.
Clone the repo if not already done. Make sure you are standing in the repo directory.
To build the complete site,
docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-rnaseq:latest
To build a single file (for example index.Rmd),
docker run --rm -u $(id -u ${USER}):$(id -g ${USER}) -v ${PWD}:/rmd ghcr.io/nbisweden/workshop-rnaseq:latest Rscript -e 'rmarkdown::render("index.Rmd")'
See Dockerfile to build the image.
❗ Output files are for local preview only. Do not push any rendered .html files or intermediates.
The 3-day course source material is located on the master branch (default). The 2-day course material is located on the twoday branch. 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 or twoday branches are automatically rendered to the gh-pages branch.
❗ Every push rebuilds the whole website using a docker image. Build takes about 6 mins.
2024 • NBIS • SciLifeLab