Repository contains code and files to interactive genomics Africa Dashboard

1. conda env create -f requirements.yml
2. conda (or source) activate SARS-Cov-2-Africa-dashboard

You can run the dashboard using your own data or setting up GISAID API. In order to inform your choice, set an environment variable:

• export COVID_DASHBOARD_SOURCE=metadata, to use your customized data
• export COVID_DASHBOARD_SOURCE=GISAID_API, to use GISAID API

Create your metadata based on data/template_metadata.csv and save as ./data/metadata.csv

1. Work with GISAID to get a Data Provision Agreement.
2. Define the following environment variables in your environment:

GISAID_URL
GISAID_USERNAME
GISAID_PASSWORD

4. Do the editions you need to fit your data if they differ from ours in data_process.py

Once your environment is set, run the following commands to generate the files and run the app:

1. python data_process.py
2. Rscript source/dashboard_tables.R
3. streamlit run app.py