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.
Release history Release notifications | RSS feed
Download files
Download the file for your platform. If you're not sure which to choose, learn more about installing packages.
Source Distribution
Built Distribution
Filter files by name, interpreter, ABI, and platform.
If you're not sure about the file name format, learn more about wheel file names.
Copy a direct link to the current filters
File details
Details for the file snippy_nextgen-1.7.0.tar.gz.
File metadata
- Download URL: snippy_nextgen-1.7.0.tar.gz
- Upload date:
- Size: 6.9 MB
- Tags: Source
- Uploaded using Trusted Publishing? No
- Uploaded via: python-httpx/0.28.1
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
2ef137d605fc2b7f0e33eefe6ea5c8ce8847d92705f46feffa2a8d4eaba55d54
|
|
| MD5 |
612579171cdb1264030cf5f629f2a402
|
|
| BLAKE2b-256 |
dc672cffbd0a8ec3ce5a82848d17d8edd76132466c75effc1a421b1f550483df
|
File details
Details for the file snippy_nextgen-1.7.0-py3-none-any.whl.
File metadata
- Download URL: snippy_nextgen-1.7.0-py3-none-any.whl
- Upload date:
- Size: 39.1 kB
- Tags: Python 3
- Uploaded using Trusted Publishing? No
- Uploaded via: python-httpx/0.28.1
File hashes
| Algorithm | Hash digest | |
|---|---|---|
| SHA256 |
bdd50e96e8bcf840c2a53ede11e70c5a01e668e0f6223a5ccbb3ad162ce17fec
|
|
| MD5 |
258ba27754ef318751c203d3cf3839b5
|
|
| BLAKE2b-256 |
5425fcd362a97a41a907d2886f6d63a33d2a22acadd1419bedcbcb6ecce54179
|
