Pipeline components for real-time virus analysis

Mumps build

How to run

1. Run all commands from this directory

2. Download FASTA file via fauna

Should populate fauna/data/measles.fasta.

3. Prepare analysis

python measles.prepare.py

This creates the file prepared/measles.json.

4. Run build

python measles.process.py

This creates intermediary files in processed/ and auspice-ready JSONs in auspice/ for both global build.

5. Copy JSONs to auspice

cp auspice/measles_* ../../../auspice/data/

6. Run auspice to visualize

cd ../../../auspice
npm run start:local