CERI-KRISP/SARS-Cov-2-Africa-dashboard

# SARS-COV-2 Africa dashboard Repository contains code and files to interactive genomics Africa Dashboard ## How to install: 1. `conda env create -f requirements.yml` 2. `conda (or source) activate SARS-Cov-2-Africa-dashboard` ## Data 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 ### Using metadata Create your metadata based on data/template_metadata.csv and save as `./data/metadata.csv` ### Using GISAID API 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 ## Running the app 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`