ChildhoodCancerDataInitiative-cBioPortal-Workflows

CCDI Prefect Workflows for data transformation, ingestion and export to/from CCDI cBioPortal

Prerequisites

• Python 3.9+
• MySQL client tools (mysqldump)
• AWS credentials with access to:
  • AWS Secrets Manager
  • S3 bucket

Installation

1. Clone this repository
2. Install dependencies:

pip install -r requirements.txt

Workflows

• cbio-mysql-dump: A Prefect workflow that can create a MySQL database dump of cBioPortal data from a specified env/tier (e.g. dev, qa, prod etc.) and save the mysql dump to a specified S3 bucket.