raulibi2013/dada2 repository overview

This container provides a comprehensive, ready-to-use environment for Metabarcoding and Microbiome analysis. It features a pre-configured R Kernel, JupyterLab, and industry-standard bioinformatic tools, eliminating the "dependency hell" often associated with these installations.

⁠🧪 Included Tools

⁠🚀 Quick Start Guide

⁠1. Pull the Image

docker pull raulibi2013/dada2

⁠2. Run the Container

To ensure your work is saved outside the container, mount a local directory to the /work folder. Replace $(pwd) with your local path:

docker run --rm -p 8888:8888 \
    -v "$(pwd)":/home/jovyan/work \
    raulibi2013/dada2

⁠3. Access JupyterLab

Once the container is running, open your browser and navigate to: 👉 http://127.0.0.1:8888/lab?token=dada2⁠

🛠 Alternative Usage in Console Mode (Bash)

If you need to use the terminal directly in your computer:

docker run --rm -it -v "$(pwd)":/home/jovyan/work raulibi2013/dada2 bash

Download Data from Google Drive

The image includes gdown to simplify downloading large datasets directly into your workspace:

# Inside a Jupyter terminal or notebook cell
gdown --id YOUR_FILE_ID

📋 Configuration Notes

• Access Token: dada2

• Working Directory: Always save your notebooks and data in /home/jovyan/work to ensure they persist on your physical machine after the container stops.

• R Kernel: When opening JupyterLab, select the R icon from the Launcher to start your analysis.

• Hardware Requirements: Since PICRUSt2 and DADA2 are memory-intensive, it is highly recommended to allocate at least 8GB of RAM in your Docker Desktop settings.