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.

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📌 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 download 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

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🚀 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.

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📂 Jupyter Notebooks

The notebooks folder contains three Jupyter notebooks:

• Hail_tutorial-GWAS-vcf.ipynb:
  A complete GWAS analysis using a VCF file.
• Hail_tutorial-GWAS-vcf-medium.ipynb:
  A medium-scale example of GWAS analysis.
• Hail_tutorial_GWAS_vcf_mini.ipynb:
  A minimal version with essential GWAS code.

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⚠️ 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