Docker Installation for GLUE on Windows

Docker Installation for GLUE on Windows

GLUE can be installed and run on Windows systems using Docker. This approach avoids many of the manual installation difficulties associated with native installation, particularly on Windows systems. Below are the steps required to set up Docker and install GLUE on Windows.

Prerequisites

To install and run Docker on a Windows machine, ensure that you meet the following requirements:

• Windows 10 (64-bit) with WSL2 enabled.
  • WSL2 (Windows Subsystem for Linux v2) allows running a Linux environment on Windows without a virtual machine.

You can find the official GLUE installation instructions here, but this guide will focus specifically on using Docker.

Step 1: Install Docker for Windows

1. Download Docker Desktop for Windows from the Docker Hub.
   Note: This requires Windows 10 64-bit with WSL2.

2. Follow the installation steps and ensure that Docker Desktop is configured to use WSL2 as the default backend.

Step 2: Enable WSL2 on Windows

If WSL2 is not already installed, follow these steps:

1. Enable WSL2:

   • Open PowerShell as Administrator and run the following command:

dism.exe /online /enable-feature /featurename:Microsoft-Windows-Subsystem-Linux /all /norestart

2. Enable Virtual Machine Platform:

• Run the following command in PowerShell:

dism.exe /online /enable-feature /featurename:VirtualMachinePlatform /all /norestart

3. Restart your computer.

4. Install the WSL2 Linux kernel update package for x64 machines from the Microsoft website.

5. Open PowerShell and set WSL2 as the default version:

wsl --set-default-version 2

6. Install your preferred Linux distribution (e.g., Ubuntu 20.04 LTS) from the Microsoft Store.

7. Once installed, launch the Linux distribution and create a username and password. Note: Usernames should be lowercase, and passwords are not displayed when typing (but will prompt for confirmation).

Step 3: Install Docker Desktop with WSL2 Support

1. Download and install Docker Desktop from the link provided above. During installation, ensure the following options are enabled:

   • Use the WSL 2-based engine
   • Add Docker to the Windows PATH

2. After installation, Docker will automatically integrate with your installed Linux distribution (e.g., Ubuntu).

Step 4: Install GLUE using Docker

Now that Docker is set up, you can install GLUE by following these steps:

1. Pull the MySQL image for GLUE:

   • Open a command prompt (cmd) and enter the following command:

docker pull cvrbioinformatics/gluetools-mysql:latest

2. This command pulls the latest MySQL Docker image, which is necessary for running GLUE's database.- Run the MySQL container:

   • Start a new MySQL container by entering:

docker run --detach --name gluetools-mysql cvrbioinformatics/gluetools-mysql:latest

3. This command runs MySQL in a background container (a lightweight, isolated process that provides the database services GLUE relies on).- Pull the GLUE image:

   • To pull the latest version of GLUE, run the following command:

docker pull cvrbioinformatics/gluetools:latest

4. This downloads the Docker image containing the GLUE tools along with dependencies such as RAxML and MAFFT.- Run the GLUE container:

   • Start a new GLUE container using the following command:

docker run --rm -it --name gluetools --link gluetools-mysql cvrbioinformatics/gluetools:latest

5. This command starts GLUE in an interactive mode, linking it to the MySQL container you started earlier.

Step 5: Configure and Use GLUE

With GLUE running in Docker, you can now configure it for your project. Follow the standard setup process for your specific GLUE project, such as setting up a HEV project, by following the instructions at the GLUE installation guide.

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