ipr 1.0.0

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IPR

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.

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 -e .[dev]

Run the tests

pytest tests

Generating the Documentation

This documentation is generated using mkdocs, mkdocs-material, and markdown_refdocs.

First install the documentation dependencies

pip install .[doc]

Then generate the user manual files

markdown_refdocs ipr -o docs/reference
mkdocs build

There should now be static html files under build-docs. To view the files, serve the folder using the built-in python http server

python3 -m http.server -d build-docs