The Next Generation of Microbial Variant Calling with Snippy
Project description
Snippy-NG
🚨 Snippy-NG is under construction and should not replace Snippy 🚨
Table of Contents
Installation
snippy is available on PyPI and can be installed using pip (without external dependencies):
pip install snippy-nextgen
The complete snippy-ng environment (including all dependencies) can be installed using the snippy-ng installer script. This script will install the latest version of snippy-ng and all its dependencies.
curl -sSL https://cpg.org.au/snippy-ng/install.sh | bash -s -- --force
Development
To set up a development environment, clone the repository and install pixi and hatch. Pixi is used to manage external dependencies, and Hatch is used to manage the Python package development.
git clone git@github.com:centre-pathogen-genomics/snippy-ng.git && cd snippy-ng
# install pixi if not already installed
curl -fsSL https://pixi.sh/install.sh | bash
# install hatch if not already installed
pixi global add hatch
Activate the pixi environment and launch a hatch shell. THis will install all dependencies and set up the development environment.
pixi shell
hatch shell
snippy-ng --help
License
snippy-ng is distributed under the terms of the MIT license.
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