Real-time tracking of influenza evolution


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.

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 from auspice/.
  3. Compile site with Jekyll by running jekyll build from within the auspice/ directory. This creates a _site/ directory containing compiled resources.


Website is hosted on Amazon S3. Deploy with s3_website push from within the auspice/ directory. This pushes the _site/ directory to the specified S3 bucket. S3 credentials are stored in ENV as S3_BUCKET, S3_KEY and S3_SECRET. Environment variables can be updated locally without fear of committing private information.

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.