Clinical Genomics command center
Project description
cg
cg
stands for Clinical Genomics; a clinical sequencing platform under SciLifeLab
This is our main package for interacting with data and samples that flow through our pipeline. We rely on a set of specialized "apps" to deal with a lot of complexity like:
- Trailblazer: Python wrapper around [MIP][mip], a rare disease genomics pipeline
- Housekeeper: storage, retrieval, and archival of files
- Genotype: managing genotypes for detecting sample mix-ups
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
- CLI for interactions on the command line
Contributing
Please check out our guide for contributing to cg
Installation
Cg written in Python 3.6+ and is available on the Python Package Index (PyPI).
pip install cg
If you would like to install the latest development version:
git clone https://github.com/Clinical-Genomics/cg
cd cg
To install CG either use pipenv (as described in contributing) and run
pipenv install -e .
or (without pipenv)
pip install -r requirements-dev.txt --editable .
Files will be blacked automatically with each push to github. If you would like to automatically Black format your commits on your local machince:
pre-commit install
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