BioGITOM_Installation.md

Installation

Follow the steps below to install and set up BioGITOM:

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1. Clone the BioGITOM Repository

Clone the repository from GitHub to your local system:

git clone https://github.com/lias-laboratory/biogitom.git

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2. Navigate to the Project Directory

Change to the directory where the repository was cloned:

cd biogitom

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3. Set Up a Virtual Environment (Recommended)

Using a virtual environment ensures that dependencies do not conflict with other Python projects. Create and activate a virtual environment as follows:

• Create the Environment:

  python -m venv env

• Activate the Environment:

  • On Linux/Mac:

    source env/bin/activate

  • On Windows:

    env\Scripts\activate

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4. Install Dependencies

Once the virtual environment is activated, install the required dependencies:

pip install -r requirements.txt

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5. Download the Required Data

Run the following script to download and extract the required data files:

python download_data.py

• What this script does:
  • Downloads a compressed archive of the required data files from the remote server.
  • Extracts the files into a temporary temp/ directory.
  • Moves the files to the appropriate locations within the repository (e.g., Datasets/, Tasks/).
  • Deletes the temporary temp/ directory after extraction.

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By following these steps, BioGITOM will be ready for use! For guidance on executing tasks and running experiments, refer to the Reproducibility Guide section.