agvd-docs

This site holds documentation for the AGVD (African Genomic Variation Database) frontend. It uses github pages, following this tutorial: Setting up github pages

Jekyll stuff

setup on a new machine (Ubuntu in this case) WIP

sudo apt-get install ruby-full build-essential zlib1g-dev

echo '# Install Ruby Gems to ~/gems' >> ~/.bashrc
echo 'export GEM_HOME="$HOME/gems"' >> ~/.bashrc
echo 'export PATH="$HOME/gems/bin:$PATH"' >> ~/.bashrc
source ~/.bashrc

bundle install 

# if `bundle install` fails
# run `gem install <packagename>` on each gem with an error


# serve locally
cd ./docs
bundle exec jekyll serve

Overriding theme defaults

Note:

• GitHub Pages use a specific version of minima (currently v2.5.1) listed here
• here are instructions for customising it

# find the installed theme's path eg 'minima'
bundle info --path minima

# copy the files you want to change
mkdir _includes
mkdir _layouts

# eg
cp $GEM_HOME/gems/minima-2.5.1/_layouts/* _layouts/
cp $GEM_HOME/gems/gems/minima-2.5.1/_includes/footer.html _includes/
cp $GEM_HOME/gems/gems/minima-2.5.1/_includes/head.html _includes/
cp $GEM_HOME/gems/gems/minima-2.5.1/_includes/header.html _includes/

References:

• Leaflet map styles
• Using the Stadia API for map tiles
• Customizing leaflet

Note on AGVD Tutorials

Because the tutorials will be updated frequently, we're going edit in Google docs.

Current tutorials are:

• Registering
• Searching

The steps are:

1. edit the google doc
2. download as pdf
3. copy this pdf to ./docs/tutorials (and rename to short name)

Full documentation here