cg 51.5.3

Clinical Genomics command center

cg

cg stands for Clinical Genomics; a clinical sequencing platform under SciLifeLab

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 .