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_includes
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README.md
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module1.md
module2.md
module3.md
praise.md
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README.md

BIOINF 525: Foundations of Bioinformatics and Systems Biology

BIOINF525 course website for 2016, see: http://bioboot.github.io/bioinf525_w16/

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 bioinf525_w16 GitHub repo) you will need to have the jekyll and github-pages gem setup, i.e.:

Consider updating RubyGems first (likely 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 day{2,3,4,5}.md files 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/bioinf525_w16.git
cd web-2015

## Edit your files (e.g. module3.md)
vi module3.md

## Check changes localy
jekyll serve

## Pull recent changes
git pull origin gh-pages

## Stage, commit and push your changes
git status
git add module3.md
git commit -m "Your msg about changes"
git push origin gh-pages

How this site was built

Basic setup entailed:

jekyll new 2015
cd 2015
## Edited site title, description etc. in _config.yml
vi _config.yml  
rm -rf _posts/   ##  we are not going to have a blog
mv index.html blog.html  ## can delete later

Create a simple index.md file and have a quick look with 'jekyll serve'

jekyll serve

After some more content addition I then followed the instructions for adding to GitHub pages.

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