Real-time tracking of influenza evolution

Auspice

Note: As of Sep 2017, this JavaScript app is deprecated in favor of nextstrain/auspice. The code in this directory is kept in place for archival reasons.

Website for visualizing and interacting with phylogenies produced augur pipeline. Interactive visualization is done with d3.js.

Install

Install all dependencies by running:

sudo gem install bundler
bundle install

NOTE: This will probably fail with error messages. There are often problems with installations of libv8 and therubyracer. Run the following after the error messages:

sudo gem uninstall libv8
sudo gem install therubyracer -v '0.12.2'
sudo gem install libv8 -v '3.16.14.17' -- --with-system-v8
bundle install

Build and compile

  1. Build JSONs via augur. These will be exported to augur/flu/auspice/. Move JSON files to auspice/data/.
  2. Create index files by running python provision_directories.py from auspice/.
  3. Compile site with Jekyll by running jekyll build from within the auspice/ directory. This creates a _site/ directory containing compiled resources.

Deployment

Website is hosted on Netlify. Use the Netlify CLI to deploy the build by running:

netlify deploy --build --prod

NOTE: Be sure to include the --build option as this runs the build command within netlify.toml to replace the placeholder username and passwords with the environment variables set in Netlify.

Local development

Develop locally by running jekyll serve and then going to http://localhost:4000/ in the browser. Jekyll will recompile as local files are modified.