{"repo":"Sage-Bionetworks/Genie","free":true,"listed":false,"github":"https://github.com/Sage-Bionetworks/Genie","clone":"git clone https://github.com/Sage-Bionetworks/Genie.git","description":"Validation and processing of GENIE files","language":"Python","stars":15,"topics":["genie","componc","python","etl","dpe"],"license":"MIT","category":"data-pipelines","readme_excerpt":"AACR Project GENIE Table of Contents - Introduction - Documentation - Dependencies - File Validator - Contributing - Sage Bionetworks Only - Running locally - Using conda - Using pipenv - Using docker ( HIGHLY Recommended) - Setting up - Developing - Developing with Docker - Modifying Docker - Testing - Running unit tests - Running integration tests - Production - Github Workflows Introduction This repository documents code used to gather, QC, standardize, and analyze data uploaded by institutes participating in AACR's Project GENIE (Genomics, Evidence, Neoplasia, Information, Exchange). Documentation For more information about the AACR genie repository, visit the GitHub Pages site. Dependencies This package contains both R, Python and cli tools. These are tools or packages you will need, to be able to reproduce these results: - Python =3.10 or <3.12 - pip install -r requirements.txt - bedtools - R 4.3.3 - renv::install() - Follow instructions here to install synapser - Java = 21 - For mac users, it seems to work better to run brew install java - wget - For mac users, have to run brew install wget File Validator Please see the local file validation tutorial for more information on this and how to use it. Contributing Please view contributing guide to learn how to contribute to the GENIE package. Sage Bionetworks Only Running locally These are instructions on how you would setup your environment and run the pipeline locally. 1. Make sure you have read through the GENIE Onboard","default_branch":null,"files":null,"tree":[],"storefront":"/r/Sage-Bionetworks","claimed":false,"request_supported":{"post":"https://gitbuyer.com/r/Sage-Bionetworks/Genie/request-supported","requests":0},"note":"indexed from public GitHub; nothing is for sale on this page. Clone it from GitHub. Paid listings live at /search."}