Installation

To streamline the installation process and avoid potential software conflicts, we utilize Docker. Docker allows us to package all necessary components inside a container, ensuring consistency across different environments.

Install Docker

Windows / macOS:
1. Visit the Docker Desktop download page and download the installer for your operating system.
2. Follow the installation instructions provided on Docker’s website.
3. Once installed, launch Docker Desktop and ensure it is running.
Linux:
1. Follow the Docker Linux installation guide for your distribution (e.g., Ubuntu, CentOS).
2. Start the Docker service using:
```
sudo systemctl start docker
```
3. Optionally, enable Docker to start at boot:
```
sudo systemctl enable docker
```

Pull the Docker Image for Proviral Analysis

With Docker installed and running, you can now download the pre-configured Docker image that contains the proviral sequence analysis pipeline:

Open your terminal or command prompt and execute the following command:
```
docker pull cfelab/proviral
```
This command downloads the latest version of the Docker image from the repository. To test the image, execute:
```
docker run --rm cfelab/proviral --version
```
You should see a version number like this:
```
Proviral Pipeline 2.4.0
```

Next: data preparation.