This repo contains the material for NBIS workshop Analysis of RNA-Seq data. The rendered view of this repo is available here.
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.
The first build can take around 30-40 mins depending on the number of R packages. Subsequent builds take about 2 minutes since caching is enabled. Caches are removed after 7 days of last access. A push after that will require a full rebuild.
For more details about repo organisation, updating and modifying this repo, check out the template repo.
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.
The website is automatically rendered by GitHub Actions whenever a change is pushed. DO NOT push any rendered material such as slide_topic.html, lab_topic.html or supporting directories slide_topic_files, lab_topic_files etc to GitHub.
For local rendering, you need R installed on your system along with dependency packages listed under packages_cran_repo and packages_bioc_repo in _site.yml. Steps below are run in R.
Run rmarkdown::render_site() in the project directory. This renders all .Rmd and .md files to generate the HTML files and all other necessary files (including the assets, images and data directories) and moves them all into a directory specified under output_dir in _site.yml. Open output_dir/index.html to start. Remove this directory after use. DO NOT commit and push this output directory to GitHub.
You can also run rmarkdown::render("bla.Rmd") on individual .Rmd/.md files. This is a time-saver as the whole website need not be rendered just to preview this one file.
2020 NBIS • SciLifeLab