Guide to Running Docker with Notebooks and Data

This guide outlines the steps to pull a Docker image, mount necessary directories (such as notebooks, data, and results), and run the container using Docker.

Platform-Specific Requirements

Windows

• Install Docker Desktop:
  1. Download Docker Desktop from https://www.docker.com/products/docker-desktop.
  2. Follow the on-screen instructions to install.
  3. Launch Docker Desktop and ensure it is running.

macOS

• Install Docker Desktop:
  1. Download Docker Desktop from https://www.docker.com/products/docker-desktop.
  2. Follow the installation instructions and start Docker Desktop.

Linux

• Install Docker Engine:
  1. Update your package manager and install Docker. For example, on Ubuntu:

     sudo apt-get update
     sudo apt-get install -y docker.io
     sudo systemctl start docker
     sudo systemctl enable docker
     

  2. Add your user to the docker group to avoid using sudo with Docker commands:

     sudo usermod -aG docker $USER
     newgrp docker
     

Note: Make sure you are running Docker Desktop or started your docker engine before performing any of the commands below.

Step 1: Pull the Docker Image

First, you need to pull the Docker image from the registry (e.g., Docker Hub). Use the following command to pull the image:

docker pull ghcr.io/bioinfodlsu/metagenomics-workshop/deploy:latest

This command fetches the image and prepares it for running in a container.

Step 2: Mount Local Directories

You’ll want to mount your local directories to the Docker container to ensure that your notebooks, data, and results are accessible inside the container.

Here’s a breakdown of the directories being mounted:

• Data: Your local path path_to_your_data_directory containing the data will be mounted to /home/jovyan/data in the container. The data should be downloaded from the data folder located in this Drive Link (https://drive.google.com/drive/folders/1pfcwepIvSYmJ_wBp668jbVYR8nekrSF3?usp=sharing). Ensure that the required data files are placed in this directory before running the container.
• Notebooks: Your local path path_to_your_notebooks_directory will be mounted to /home/jovyan/notebooks in the container. The notebooks should be downloaded from the notebooks folder in the Github repository provided. Place your Jupyter notebooks into this local directory before running the container.

Make sure your data and notebooks are placed in your specified local directories before running the container.

Step 3: Run the Docker Container

Once the image is pulled and your directories are set up, run the Docker container with the following command:

docker run -p 8888:8888 -v "path_to_your_data_directory:/home/jovyan/data" -v "path_to_your_notebooks_directory:/home/jovyan/notebooks" ghcr.io/bioinfodlsu/metagenomics-workshop/deploy:latest

Note: Please remember to replace the paths with your corresponding data and notebook directories.

Step 4: Access Jupyter Notebook

Once the container is running, a link to the Jupyter Notebook interface, including the authentication token (e.g., http://127.0.0.1:8888/?token=your_token), will appear in the terminal or command prompt after starting the container. Simply copy and paste this link into your browser.