Skip to content

Latest commit

 

History

History
83 lines (53 loc) · 2.13 KB

README.md

File metadata and controls

83 lines (53 loc) · 2.13 KB

Hail Tutorial

This tutorial provides Jupyter notebooks based on the Hail GWAS tutorial to demonstrate how to perform a GWAS (Genome-Wide Association Study) analysis using a VCF file, while storing Hail data structures in an external S3 storage.

📌 Setting Up the Environment

To get started, clone this repository:

git clone https://github.com/crs4/hail_tutorial.git
cd hail_tutorial

Then, start the Docker environment:

docker compose up -d

On the first run, Docker will build two images:

  • hail_tutorial – The environment for running the tutorials in a Jupyter Lab server.
  • minio – A high-performance object storage service with an API compatible with Amazon S3.

To shut down the Docker containers, run:

docker compose down

🚀 Accessing the Tutorials

Jupyter Lab

  • Open a browser and go to localhost:18888.
  • Enter the password: 12345678 (only required the first time).

MinIO S3 Storage

  • Open localhost:9001 in a browser.
  • Use the credentials:
    • Username: root
    • Password: passpass

Once you run a Jupyter notebook, the data-hail bucket will be created in MinIO.

📂 Jupyter Notebooks

The notebooks folder contains two Jupyter notebooks:

⚠️ Additional Notes

  • Ensure Docker compose is installed and running before starting the environment.

  • If you encounter issues accessing Jupyter Lab, check if the container is running:

    docker compose ps

  • Restart the Docker environment if needed:

    docker compose down && docker compose up -d

  • Print logs of the Jupyter Hub service if needed:

    docker compose logs -f jupyter