Pipeline components for real-time virus analysis

Ebola build

How to run

1. Run all commands from this directory

2. Download FASTA file via fauna and prepare analysis

python ebola.prepare.py

Alternatively, supply a FASTA file with conforming headings and pass in this file with --sequences. python ebola.prepare.py --sequences example_data/ebola.fasta Running ebola.prepare.py creates the file prepared/ebola.json.

3. Run build

python ebola.process.py

This creates intermediary files in processed/ and auspice-ready JSONs in auspice/.

4. Copy JSONs to auspice

cp auspice/ebola_* ../../../auspice/data/

5. Run auspice to visualize

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