Welcome to the RaukR 2022 Teaching Materials GitHub repository.

• Fork this repository (NBISweden/RaukR-XXXX) to your GitHub (user/RaukR-XXXX).
• Clone your fork to your local computer.

• You can simply delete the assets directory and replace it with the new assets directory for presentation or lab.
• Render your .Rmd again and verify changes

• Install the R package raukrtemplate and follow instructions there to create a template on your system. Label it topic_presentation.Rmd or topic_lab.Rmd.

• When done, copy source materials (.Rmd), rendered files (.html) and all supporting files and folders to /topic/presentation/ or /topic/lab/.
• Add links to your rendered html files in index.md.
• Push the updated changes to from your local clone to your fork (user/RaukR-XXXX).

TIP: You can preview the render version of the pages on your fork (user/RaukR-XXXX). Go to user/RaukR-XXXX, Settings > Pages. Then enable GitHub pages to be hosted from the main branch and root directory and click Save. The rendered pages should be visible at user.github.io/RaukR-XXXX. This can anywhere from a few minutes to 10 mins. Remember to hard refresh (Shift) your browser.

• Then send a pull request (online) from your fork (user/RaukR-XXXX) to (NBISweden/RaukR-XXXX) and assign one of your colleagues as a reviewer.
• When you get back your reviewer's comments, address them and push changes from your local clone to your fork (user/RaukR-XXXX).
• The new updates are automatically added to your previous pull request.
• The reviewer accepts and merges the pull request (online). You can also merge it yourself for subsequent pull requests.
• Continue making your materials even better. Create a new pull request when you achieve next milestone.

• Check for typos, readability, rendering issues. Also look if something is missing in the content or give suggestions on how to improve it.
• If possible, try to run the code to check that it is reproducible.
• You can work in two ways:
  • clone your colleagues fork, work on her/his presentation slides/lab and pull request the changes that she/he will merge OR
  • just leave the comments in the pull request and let the author know.

If you add to links to your rendered html files to index.md, the content can be seen at: https://nbisweden.github.io/RaukR-2022/

If you have files larger than 100Mb in your materials, e.g. a dataset:

before you issue git add yourlargefile follow instructions here: https://git-lfs.github.com