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/mumps.fasta.

3. Prepare analyses

python mumps.prepare.py --geo global

This creates the file prepared/mumps_global.json.

python mumps.prepare.py --geo na

This creates the file prepared/mumps_na.json.

4. Run builds

python mumps.process.py --json prepared/mumps_global.json --geo global

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

python mumps.process.py --json prepared/mumps_na.json --geo na

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

5. Copy JSONs to auspice

cp auspice/mumps_* ../../../auspice/data/

6. Run auspice to visualize

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