Repository contains code and files to interactive genomics Africa Dashboard
conda env create -f requirements.yml
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 dataexport COVID_DASHBOARD_SOURCE=GISAID_API
, to use GISAID API
Create your metadata based on data/template_metadata.csv and save as ./data/metadata.csv
- Work with GISAID to get a Data Provision Agreement.
- Define the following environment variables in your environment:
GISAID_URL
GISAID_USERNAME
GISAID_PASSWORD
- 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:
python data_process.py
Rscript source/dashboard_tables.R
streamlit run app.py