https://github.com/clinical-genomics/cg

Glue between Clinical Genomics apps
https://github.com/clinical-genomics/cg

Last synced: 19 days ago
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Glue between Clinical Genomics apps

• Host: GitHub
• URL: https://github.com/clinical-genomics/cg
• Owner: Clinical-Genomics
• Created: 2017-02-20T14:29:43.000Z (almost 8 years ago)
• Default Branch: master
• Last Pushed: 2024-10-29T09:54:19.000Z (about 2 months ago)
• Last Synced: 2024-10-29T10:03:04.625Z (about 2 months ago)
• Language: Python
• Homepage:
• Size: 31.2 MB
• Stars: 8
• Watchers: 10
• Forks: 2
• Open Issues: 86
• Metadata Files:
  • Readme: README.md
  • Changelog: CHANGELOG.md
  • Contributing: CONTRIBUTING.md
  • Codeowners: .github/CODEOWNERS

Awesome Lists containing this project

README

        
# cg

![Build Status - Github][gh-actions-badge]

[![Coverage Status][coveralls-image]][coveralls-url]

[![GitHub issues-closed][closed-issues-img]][closed-issues-url]

[![Average time to resolve an issue][ismaintained-resolve-img]][ismaintained-resolve-url]

[![Percentage of issues still open][ismaintained-open-rate-img]][ismaintained-open-rate-url]

[![CodeFactor][codefactor-badge]][codefactor-url]

[![Code style: black][black-image]][black-url]

`cg` stands for _Clinical Genomics_; a clinical sequencing platform under [SciLifeLab][scilife]

In this context, `cg` provides the interface between these tools to facilitate automation and other necessary cross-talk. It also exposes some APIs:

- HTTP REST for powering the web portal: [clinical.scilifelab.se][portal]

- CLI for interactions on the command line

### Contributing

Please check out our [guide for contributing to cg](CONTRIBUTING.md)

## Installation

Cg written in Python 3.9+ and is available on the [Python Package Index][pypi] (PyPI).

```bash

pip install cg

```

If you would like to install the latest development version, use [poetry](https://python-poetry.org/docs/).

```bash

git clone https://github.com/Clinical-Genomics/cg

cd cg

poetry install

```

[portal]: https://clinical.scilifelab.se/

[trailblazer]: https://github.com/Clinical-Genomics/trailblazer

[housekeeper]: https://github.com/Clinical-Genomics/housekeeper

[genotype]: https://github.com/Clinical-Genomics/genotype

[scilife]: https://www.scilifelab.se/

[pypi]: https://pypi.org/

[black]: https://black.readthedocs.io/en/stable/

[coveralls-url]: https://coveralls.io/github/Clinical-Genomics/cg

[coveralls-image]: https://coveralls.io/repos/github/Clinical-Genomics/cg/badge.svg?branch=master

[gh-actions-badge]: https://github.com/Clinical-Genomics/cg/workflows/Tests%20and%20coveralls/badge.svg

[closed-issues-img]: https://img.shields.io/github/issues-closed/Clinical-Genomics/cg.svg

[closed-issues-url]: https://GitHub.com/Clinical-Genomics/cg/issues?q=is%3Aissue+is%3Aclosed

[ismaintained-resolve-img]: http://isitmaintained.com/badge/resolution/Clinical-Genomics/cg.svg

[ismaintained-resolve-url]: http://isitmaintained.com/project/Clinical-Genomics/cg

[ismaintained-open-rate-img]: http://isitmaintained.com/badge/open/Clinical-Genomics/cg.svg

[ismaintained-open-rate-url]: http://isitmaintained.com/project/Clinical-Genomics/cg

[codefactor-badge]: https://www.codefactor.io/repository/github/clinical-genomics/cg/badge

[codefactor-url]: https://www.codefactor.io/repository/github/clinical-genomics/cg

[black-image]: https://img.shields.io/badge/code%20style-black-000000.svg

[black-url]: https://github.com/psf/black