https://github.com/nextstrain/mumps
Nextstrain build for mumps virus
https://github.com/nextstrain/mumps
nextstrain pathogen
Last synced: 10 months ago
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Nextstrain build for mumps virus
- Host: GitHub
- URL: https://github.com/nextstrain/mumps
- Owner: nextstrain
- Created: 2018-09-01T23:33:24.000Z (over 7 years ago)
- Default Branch: main
- Last Pushed: 2025-07-08T22:44:21.000Z (11 months ago)
- Last Synced: 2025-07-08T23:34:40.092Z (11 months ago)
- Topics: nextstrain, pathogen
- Language: Python
- Homepage: https://nextstrain.org/mumps
- Size: 1.37 MB
- Stars: 2
- Watchers: 18
- Forks: 5
- Open Issues: 5
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Nextstrain repository for mumps virus
This repository contains three workflows for the analysis of mumps virus data:
- [`ingest/`] - Download data from GenBank, clean and curate it
- [`phylogenetic/`][] - Filter sequences, align, construct phylogeny,
and export for visualization
Each workflow directory contains a `README.md` file with more
information. The results of running both workflows are publicly
visible at [nextstrain.org/mumps][].
## Installation
Follow the [standard installation instructions][] for Nextstrain's
suite of software tools.
## Quick start
Run the phylogenetic workflow by executing the following commands in
the repository checkout, after installing `nextstrain` per the above
instructions:
```bash
cd phylogenetic/
nextstrain build .
nextstrain view .
```
Further documentation is available at "[Running a pathogen workflow][]".
## Working on this repository
This repository is configured to use [pre-commit][] to help
automatically catch common coding errors and syntax issues with
changes before they are committed to the repo.
If you will be writing new code or otherwise working within this
repository, please do the following to get started:
1. install `pre-commit`, by running either `python -m pip install
pre-commit` or `brew install pre-commit`, depending on your
preferred package management solution
2. install the local git hooks by running `pre-commit install` from
the root of the repository
3. when problems are detected, correct them in your local working tree
before committing them.
Note that these pre-commit checks are also run in a GitHub Action when
changes are pushed to GitHub, so correcting issues locally will
prevent extra cycles of correction.
[`ingest/`]: ./ingest
[`phylogenetic/`]: ./phylogenetic
[nextstrain.org/mumps]: https://nextstrain.org/mumps
[Running a pathogen workflow]: https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html
[pre-commit]: https://pre-commit.com
[standard installation instructions]: https://docs.nextstrain.org/en/latest/install.html