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Prerequisites

PROTÉGÉ PD runs exclusively in a Docker container. You must have Docker installed before proceeding.

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System requirements

  • Docker Desktop or Docker Engine
  • Command line interface (CLI) access
  • At least 4 CPU cores available for allocation
  • Internet connection for downloading the Docker image

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Install Docker

1

Download Docker Desktop

Select the appropriate installer for your operating system:

Linux

Docker Desktop for Linux

Windows

Docker Desktop for Windows

macOS

Docker Desktop for Mac
2

Complete installation

Follow the installation instructions for your operating system. The installer will guide you through the setup process.
3

Verify installation

After installation, verify Docker is working correctly by following the official Get started tutorial.You can also run a quick test:
docker --version
This should display your Docker version.

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Pull the PROTÉGÉ PD image

Once Docker is installed, download the PROTÉGÉ PD image from Docker Hub: 
docker pull ddelgadillo/protege_base:v1.0.2
The image includes Python 3.10, BioPython, MUSCLE aligner, Dash web framework, and all required dependencies. You don’t need to install anything else.
The download may take several minutes depending on your internet connection. Docker will display progress bars for each layer being downloaded.

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Verify the installation

After pulling the image, verify it’s available: 
docker images | grep protege
You should see output similar to: 
ddelgadillo/protege_base   v1.0.2    [IMAGE_ID]   [SIZE]

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What’s included

The PROTÉGÉ PD Docker image contains:
  • Python 3.10 with scientific computing libraries
  • BioPython 1.83 for sequence manipulation and melting temperature calculations
  • MUSCLE alignment tool for protein sequence alignment
  • Dash 2.14.2 for the interactive web interface
  • Plotly 5.18.0 for visualization
  • NumPy, Pandas, and SciPy for data processing
Make sure you have sufficient disk space available. The Docker image requires approximately 1-2 GB of storage.

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Troubleshooting

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Docker daemon not running

If you encounter errors about the Docker daemon not being available:
  1. Start Docker Desktop from your applications menu
  2. Wait for Docker to fully initialize (check the system tray icon)
  3. Try the command again

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Permission denied errors (Linux)

On Linux, you may need to add your user to the docker group: 
sudo usermod -aG docker $USER
Log out and back in for the changes to take effect.

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Image pull fails

If the image fails to download:
  • Check your internet connection
  • Verify you have enough disk space
  • Try pulling the image again (Docker will resume from where it stopped)

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Next steps

Quickstart Guide

Learn how to run PROTÉGÉ PD and design your first primers

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