OncoProExp

OncoProExp is a Shiny-based web application for analyzing cancer proteomic and phosphoproteomic data using statistical methods and advanced AI-based models. This repository contains the source code, Dockerfile, and installation scripts necessary to deploy the application locally.

Prerequisites

• Docker (ensure Docker is installed and running on your machine)
• Git (to clone the repository)
• Make sure that you have a sudo privilege during the installtion process

Installation

1. Clone the Repository

Open a terminal and run:

git clone https://gitlab.cs.ut.ee/edris/oncoproexp.git
cd oncoproexp

2. Build the Docker Image

Build the Docker image using the provided Dockerfile. In the repository root directory, run:

docker build -t oncoproexp:latest .

This command builds an image named oncoproexp tagged as latest based on the instructions in the Dockerfile. The Dockerfile installs the required system dependencies, R packages (via installation.R), and configures the Shiny server.

3. Run the Docker Container

After the image is built, run a container locally with:

docker run -d -p 3838:3838 oncoproexp:latest

This command runs the container in detached mode (-d) and maps port 3838 of the container to port 3838 on your host machine.

4. Access the Application

Open your web browser and navigate to:

http://localhost:3838

You should see the OncoProExp Shiny application running.

Additional Notes

• Ports:
  The container exposes ports 80 and 3838. By default, the Shiny app is run on port 3838.

• Stopping the Container:
  To stop the container, list running containers with:

  docker ps

  Then stop the desired container using:

  docker stop <container_id>

Troubleshooting

• If you encounter issues during the build process, review the output logs to identify missing dependencies or package installation errors.
• Make sure Docker has enough resources allocated (CPU, RAM) to build and run the container successfully.

License

GPL-2 | GPL-3 [expanded from: GPL]