faruqsandi / pori_ipr_python

Python adapter for generating reports uploaded to IPR using the PORI platform

IPR

This repository is part of the Platform for Oncogenomic Reporting and Interpretation (PORI).

This python tool takes in variant inputs as tab-delimited files and annotates them using GraphKB. The resulting output is uploaded to IPR as a report. Additional report content such as images and metadata can be passed to be included in the report upload.

For documentation on how to create reports using this adaptor, see the main documentation site for the platform.

Getting Started

Install (For developers)

clone this repository

git clone https://github.com/bcgsc/pori_ipr_python.git
cd pori_ipr_python

create a virtual environment

python3 -m venv venv
source venv/bin/activate

install the package and its development dependencies

pip install -U pip setuptools
pip install -e .[dev]

Run the tests

pytest tests

Documentation

The user documentation for this tool is hosted with the main documentation site.

Developers: Any updates to this tool should be edited and reflected in the main site documentation as well.