Flu frequencies

Estimating flu clade and mutation frequencies

branch	URL
release	https://flu-frequencies.vercel.app/
master	https://master-flu-frequencies.vercel.app/

Development

This README is for the data analysis pipeline. For the web interface, see web/README.md.

Setup

Using Nextstrain CLI

Currently not working due to lack of polars in Nextstrain managed environments (conda/docker)

Install Nextstrain CLI

On Linux:

curl -fsSL --proto '=https' https://nextstrain.org/cli/installer/linux | bash

On macOS:

curl -fsSL --proto '=https' https://nextstrain.org/cli/installer/mac | bash

Setup Nextstrain CLI

You can set it up to use Docker or a Nextstrain managed conda environment (completely independent of any other conda environments you may have).

Using docker:

nextstrain setup --set-default docker

Using managed conda environment:

nextstrain setup --set-default conda

Run analysis

Run analysis:

nextstrain build . --profile profiles/flu

Using custom conda environment

Install conda environment:

mamba env create -f environment.yml

Activate the environment:

conda activate flu_frequencies

Run for flu using:

snakemake --profile profiles/flu

Run for SARS-CoV-2 using:

snakemake --profile profiles/SC2

Viewing results in web app

Run the following command to generate flu frequencies and copy the resulting CSV tables into data_web/inputs.

snakemake prep_web --profile profiles/flu

Generate the JSON versions of the CSV tables that the web application uses.

python scripts/web_convert.py --input-pathogens-json data_web/inputs/pathogens.json --output-dir web/public/data

Commit the updated JSON files in web/public/data to a development or base branch and push to GitHub to deploy a Preview version of the web application. Vercel deploys a web application for each commit in a pull request. You can access each deployment through the repository's Deployments page. See the web application README for more about deployment from the master and release branches.

TODO

• Provide mamba environment file for simpler setup
• Agree on formatters to use (snakefmt and black?)