huantan2 / bioinf606-2018

Biocomputing bootcamp website for 2018 http://dcmb-courses.github.io/bioinf606-2018/

bioinf606-2018

Biocomputing bootcamp website for 2018

See: http://dcmb-courses.github.io/bioinf606-2018/

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)

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 Bootcamp_2017
cd Bootcamp_2017
git clone [email protected]:bioboot/web-2016.git web-2017
cd web-2017/

Update _config.yml and index.md. IN particular, rembember to change the dates and the pre-course questionnaire and post-course evaluation forms. 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 web-2017 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/web-2017.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

Biocomputing bootcamp website for 2016

See: http://bioboot.github.io/web-2016/ asnd 2015 site setup details below.

Biocomputing bootcamp website for 2015,

See: http://bioboot.github.io/web-2015/ 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.:

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/web-2015.git
cd web-2015

## Edit your files (e.g. day2.md)
vi day2.md

## Check changes localy
jekyll serve

## Pull recent changes
git pull origin gh-pages

## Stage, commit and push your changes
git status
git add day2.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.

Cloned from Barry Grant (http://thegrantlab.org/) repository at https://github.com/bioboot/web-2017