From 4a79b48e11f16d6a4eb7b6d5dd75bd40507edf09 Mon Sep 17 00:00:00 2001 From: Eleanor Lewis Date: Mon, 8 Jul 2024 14:22:45 -0700 Subject: [PATCH 1/2] update readme --- README.md | 66 ++++++++++--------------------------------------------- 1 file changed, 12 insertions(+), 54 deletions(-) diff --git a/README.md b/README.md index fd592ef..76c52c1 100644 --- a/README.md +++ b/README.md @@ -1,15 +1,22 @@ -# IPR +# PORI Python Adaptor -![build](https://github.com/bcgsc/pori_ipr_python/workflows/build/badge.svg) [![PyPi](https://img.shields.io/pypi/v/ipr.svg)](https://pypi.org/project/ipr) [![codecov](https://codecov.io/gh/bcgsc/pori_ipr_python/branch/master/graph/badge.svg)](https://codecov.io/gh/bcgsc/pori_ipr_python) [![PyPI - Downloads](https://img.shields.io/pypi/dm/ipr)](https://pypistats.org/packages/ipr) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5730671.svg)](https://doi.org/10.5281/zenodo.5730671) +![build](https://github.com/bcgsc/pori_python/workflows/build/badge.svg) [![codecov](https://codecov.io/gh/bcgsc/pori_python/branch/master/graph/badge.svg)](https://codecov.io/gh/bcgsc/pori_python) This repository is part of the [Platform for Oncogenomic Reporting and Interpretation (PORI)](https://bcgsc.github.io/pori/). +This is a python adaptor package for querying the GraphKB API and IPR API. + 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](https://bcgsc.github.io/pori/) for the platform. +For documentation on how to create reports using the IPR adaptor, see the [main documentation site](https://bcgsc.github.io/pori/) for the platform. For the GraphKB adaptor, see the [user manual](https://bcgsc.github.io/pori/graphkb/scripting/) + +- [Getting Started](#getting-started) + - [Install (For developers)](#install-for-developers) +- [Documentation](#documentation) +- [Deployment (Publishing)](#deployment-publishing) ## Getting Started @@ -18,8 +25,8 @@ For documentation on how to create reports using this adaptor, see the [main doc clone this repository ```bash -git clone https://github.com/bcgsc/pori_ipr_python.git -cd pori_ipr_python +git clone https://github.com/bcgsc/pori_python.git +cd pori_python ``` create a virtual environment @@ -49,55 +56,6 @@ 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. -# GraphKB (Python) - -![build](https://github.com/bcgsc/pori_graphkb_python/workflows/build/badge.svg) [![PyPi](https://img.shields.io/pypi/v/graphkb.svg)](https://pypi.org/project/graphkb) [![codecov](https://codecov.io/gh/bcgsc/pori_graphkb_python/branch/master/graph/badge.svg)](https://codecov.io/gh/bcgsc/pori_graphkb_python) [![PyPI - Downloads](https://img.shields.io/pypi/dm/graphkb)](https://pypistats.org/packages/graphkb) [![DOI](https://zenodo.org/badge/DOI/10.5281/zenodo.5730523.svg)](https://doi.org/10.5281/zenodo.5730523) - -This repository is part of the [platform for oncogenomic reporting and interpretation](https://github.com/bcgsc/pori). - -Python adapter package for querying the GraphKB API. See the [user manual](https://bcgsc.github.io/pori/graphkb/scripting/) - -- [Getting Started](#getting-started) - - [Install (For developers)](#install-for-developers) - - [Run Tests](#run-tests) -- [Generating the Documentation](#generating-the-documentation) -- [Deployment (Publishing)](#deployment-publishing) - -## Getting Started - -### Install (For developers) - -clone this repository - -```bash -git clone https://github.com/bcgsc/pori_graphkb_python -cd pori_graphkb_python -``` - -create a virtual environment - -```bash -python3 -m venv venv -source venv/bin/activate -``` - -install the package and its development dependencies - -```bash -pip install -U pip setuptools -pip install -e .[dev] -``` - -### Run Tests - -```bash -pytest tests -``` - -## Generating the Documentation - -User documentation for this repository is hosted in the [central PORI repository](https://github.com/bcgsc/pori/) - ## Deployment (Publishing) Install the deployment dependencies From c82b51b3dcf0e3fdad1a95d188efe1bb48204eef Mon Sep 17 00:00:00 2001 From: Eleanor Lewis Date: Mon, 8 Jul 2024 14:55:40 -0700 Subject: [PATCH 2/2] fix period --- README.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/README.md b/README.md index 76c52c1..5be91c7 100644 --- a/README.md +++ b/README.md @@ -11,7 +11,7 @@ This python tool takes in variant inputs as tab-delimited files and annotates th 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 the IPR adaptor, see the [main documentation site](https://bcgsc.github.io/pori/) for the platform. For the GraphKB adaptor, see the [user manual](https://bcgsc.github.io/pori/graphkb/scripting/) +For documentation on how to create reports using the IPR adaptor, see the [main documentation site](https://bcgsc.github.io/pori/) for the platform. For the GraphKB adaptor, see the [user manual](https://bcgsc.github.io/pori/graphkb/scripting/). - [Getting Started](#getting-started) - [Install (For developers)](#install-for-developers)