Real-time tracking of influenza evolution


Website for visualizing and interacting with phylogenies produced by the nextstrain/augur pipeline. Interactive visualization is done with d3.js. This is v1 of auspice and is in maintenance mode. Active development is continuing on v2 of auspice at nextstrain/auspice.

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.