Installation Guide

This guide will help you set up the environment and install the necessary tools for using the MonViso Reloaded package.

Requirements

Before proceeding with the installation, ensure you have the following prerequisites:

  • Python 3.9: The core language used for the project.
  • Cobalt: A multiple sequence alignment tool. Download from NCBI Cobalt.
  • HMMER: Software for searching sequence databases for sequence homologs. Available at HMMER.
  • Modeller: Used for homology or comparative modeling of protein three-dimensional structures. Download from Modeller.
  • PeSTO A parameter-free geometric deep learning method to predict protein interaction interfaces from a protein structure. Clone from github.

Installation Steps

Follow these steps to install the necessary tools and the MonViso Reloaded package:

1. Install Dependencies

  • HMMER: Follow the installation instructions provided on the HMMER website.
  • COBALT: Refer to the Cobalt download page for detailed installation instructions.
  • MODELLER: Visit the Modeller website for installation guides tailored to your operating system.
  • PeSTo

2. Check Python Version

Ensure you have Python 3.9 installed by running the following command in your terminal:

python --version

3. Install via pip

pip install monviso

Verifying the installation

After completing the installation steps, verify that the MonViso Reloaded package and all dependencies are correctly installed by running a quick test command or script provided by the package documentation.

Alternative - Clone the GitHub Repository

Clone the MonViso Reloaded repository to your local machine:

git clone https://github.com/alisamalb/monviso_reloaded
cd monviso_reloaded

Install the package by executing:

python setup.py install

Alternative - Run the Docker container

  1. Download the Containerfile: First, you need to download the Containerfile. Save the file from this URL: Containerfile.

  2. Build the Docker Image: If you have a valid Modeller license, you can now build your Docker image. Open a terminal and run the following command in the directory where the Containerfile is located:

docker build --build-arg MODELLER_LICENSE=yourmodellerlicensehere -t monviso -f Containerfile .

Replace 'yourmodellerlicensehere' with your modeller license. This command builds a Docker image named monviso using the instructions in your Containerfile.

  1. Run the Container with a Mounted Working Directory: If you wish to use your own working directory (e.g., /Work) inside the container, you can do so by mounting it when you start the container. Run the following command to start the container and access your working directory within it:
docker run -it -v /Work:/Monviso/Work monviso

Replace /Work with the path to your actual working directory on the host machine. This command mounts your host directory /Work to /Monviso/Work inside the container, allowing you to work with your files directly from within the container environment.

By following these steps, you'll have a fully functional Monviso environment set up and ready to use in Docker, complete with your required Modeller license and access to your working directory.