https://github.com/nextstrain/flu_frequencies
Flu clade and mutation frequencies
https://github.com/nextstrain/flu_frequencies
clades flu influenza mutations
Last synced: 5 months ago
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Flu clade and mutation frequencies
- Host: GitHub
- URL: https://github.com/nextstrain/flu_frequencies
- Owner: nextstrain
- Created: 2023-02-12T11:12:16.000Z (over 2 years ago)
- Default Branch: master
- Last Pushed: 2024-08-26T17:15:05.000Z (9 months ago)
- Last Synced: 2024-08-26T20:22:44.289Z (9 months ago)
- Topics: clades, flu, influenza, mutations
- Language: TypeScript
- Homepage: https://flu-frequencies.vercel.app
- Size: 127 MB
- Stars: 3
- Watchers: 10
- Forks: 3
- Open Issues: 9
-
Metadata Files:
- Readme: README.md
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README
# 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](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:
```bash
curl -fsSL --proto '=https' https://nextstrain.org/cli/installer/linux | bash
```
On macOS:
```zsh
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:
```bash
nextstrain setup --set-default docker
```
Using managed conda environment:
```bash
nextstrain setup --set-default conda
```
##### Run analysis
Run analysis:
```bash
nextstrain build . --profile profiles/flu
```
#### Using custom conda environment
Install conda environment:
```bash
mamba env create -f environment.yml
```
Activate the environment:
```bash
conda activate flu_frequencies
```
Run for flu using:
```bash
snakemake --profile profiles/flu
```
Run for SARS-CoV-2 using:
```bash
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`.
``` bash
snakemake prep_web --profile profiles/flu
```
Generate the JSON versions of the CSV tables that the web application uses.
```bash
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](https://github.com/nextstrain/flu_frequencies/deployments) page.
[See the web application README](https://github.com/nextstrain/flu_frequencies/blob/master/web/README.md#branches-release-and-deployment) 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?)