https://github.com/nextstrain/measles
Nextstrain build for measles virus
https://github.com/nextstrain/measles
nextstrain pathogen
Last synced: 10 months ago
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Nextstrain build for measles virus
- Host: GitHub
- URL: https://github.com/nextstrain/measles
- Owner: nextstrain
- Created: 2018-12-29T05:54:51.000Z (over 7 years ago)
- Default Branch: main
- Last Pushed: 2024-12-13T05:22:19.000Z (over 1 year ago)
- Last Synced: 2024-12-13T06:24:26.793Z (over 1 year ago)
- Topics: nextstrain, pathogen
- Language: Python
- Homepage: https://nextstrain.org/measles
- Size: 8.39 MB
- Stars: 1
- Watchers: 13
- Forks: 6
- Open Issues: 10
-
Metadata Files:
- Readme: README.md
- Changelog: CHANGES.md
Awesome Lists containing this project
README
# Nextstrain repository for measles virus
This repository contains three workflows for the analysis of measles virus data:
- [`ingest/`](./ingest) - Download data from GenBank, clean and curate it
- [`phylogenetic/`](./phylogenetic) - Filter sequences, align, construct phylogeny and export for visualization
- [`nextclade/`](./nextclade) - Create nextclade datasets
Each folder contains a README.md with more information. The results of running both workflows are publicly visible at [nextstrain.org/measles](https://nextstrain.org/measles).
## Installation
Follow the [standard installation instructions](https://docs.nextstrain.org/en/latest/install.html) for Nextstrain's suite of software tools.
After you've installed the Nextstrain CLI, you can set up measles with
nextstrain setup measles
## Quickstart
Run the default phylogenetic workflow via:
nextstrain run measles phylogenetic measles-analysis
nextstrain view measles-analysis
## Documentation
- [Running a pathogen workflow](https://docs.nextstrain.org/en/latest/tutorials/running-a-workflow.html)
## Working on this repo
This repo is configured to use [pre-commit](https://pre-commit.com),
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 repo,
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 repo
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.