wisekh6/bggn213_w21

Winter 2021 BGGN-213 class website

Foundations of Bioinformatics course website

Author and course director: Barry J. Grant ([email protected])

Foundations of Bioinformatics (BGGN-213) is a UCSD bioscience graduate course run in the Spring quarter of 2018.
For full detailes see: https://bioboot.github.io/bggn213_S18/

Overview: This is a simple jekell based static site. To view locally on your own machine (i.e. before pushing or submitting a pull request to this bioboot GitHub repo) you will need to have the jekyll and github-pages gem setup (see further below for full instructions)

View, Edit and Contribute Changes Locally

This is a simple jekell based static site.

To view locally on your own machine (i.e. before pushing or submitting a pull request to this bioboot GitHub repo) you will need to have the jekyll and github-pages gem setup, i.e.:

Install ruby, jekyll and github-pages

To be added - for now just use homebrew on mac.

Next consider updating RubyGems first (may need sudo for these).

sudo gem update --system

Then install the Jekyll Gem and the GitHub Gem

gem install jekyll
gem install github-pages

Optional: Pygments python based syntax highlighter

pip install Pygments

Basics of Jekyll websites

Jekyll websites are configured based on the contents of the various underscore prefixed files and folders. You can find out more about these here: http://jekyllrb.com/docs/structure/

However, most likely you will want to leave most of these alone and just add
content to the lectures.md file and create new files in the class-material/ directory (i.e. add lecture slides, handouts, cheat-sheets etc.)

Please remember that all content is on the gh-pages branch! So you will want to be working on this branch and push back to this branch.

A typical workflow for folks that have been added as "Collaborators" would look something like this:

## One time only clone
git clone https://github.com/bioboot/bimm143_W18.git
cd bimm143_W18

## Edit your files (e.g. lectures.md, _data/authors.yml, _config.yml)
vi lectures.md

## Check changes localy
jekyll serve

## Pull recent changes
git pull origin gh-pages

## Stage, commit and push your changes
git status
git add lectures.md
git commit -m "Your msg about changes"
git push origin gh-pages

Roll forward instructions...

To roll forward for a new years class follow the steps below (assuming you already have jekyll and github-pages setup on your local machine):

Git clone old site to a new dir

cd ~/Dropbox/Teaching
mkdir bggn213_2018
cd bggn213_2018
git clone [email protected]:bioboot/bggn213_f17.git bggn213_f18
cd bggn213_f18/

Update _config.yml, _data/authors.yml, index.md and of course lectures.md.

In particular:

• in _config.yml change all bimm143_W18 to the new course name, including title.
• in _data/authors.yml change the Course Syllabus link, logo src, and Instructional Assistant.
• in index.md update the bimm143_W18 etc links and names, syllabus link, initial course evaluation link

Also remember to change the dates and the pre-course questionnaire and post-course evaluation forms as well as the lecture dates. Go through the regular git add, git commit -m cycle. But don’t yet push to GitHub (as we will want a new repo for this years class).

On GitHub make a new repo (Use the “+” sign and name it bggn213_f18 to match your local directory name. This name matching is purely for convenience).

Then on the local machine change your remotes to point to this new repo.

git remotes -v   
git remote rm origin  

Now add our new repo and push changes:

git remote add origin [email protected]:bioboot/bggn213_f18.git  
git push -u origin gh-pages  

Then preview your new site online: https://bioboot.github.io/web-2017/ and visit the repo itself to see if everything is ship-shape: https://github.com/bioboot/web-2017