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.
clone this repository
git clone https://github.com/bcgsc/pori_ipr_python.git
cd pori_ipr_pythoncreate a virtual environment
python3 -m venv venv
source venv/bin/activateinstall the package and its development dependencies
pip install -U pip setuptools
pip install -e .[dev]Run the tests
pytest testsThe 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.
This repository is part of the platform for oncogenomic reporting and interpretation.
Python adapter package for querying the GraphKB API. See the user manual
clone this repository
git clone https://github.com/bcgsc/pori_graphkb_python
cd pori_graphkb_pythoncreate a virtual environment
python3 -m venv venv
source venv/bin/activateinstall the package and its development dependencies
pip install -U pip setuptools
pip install -e .[dev]pytest testsUser documentation for this repository is hosted in the central PORI repository
Install the deployment dependencies
pip install .[deploy]Build the distribution files
python setup.py install sdist bdist_wheelUpload the distibutions to the package server (-r is defined in your pypirc)
twine upload -r bcgsc dist/*