Installing the pipeline

It is recommended to use a Python virtual environment to reduce the risk of any Python package conflicts.

HPC Workstation or Local PC

  1. Create a Python virtual environment
    The Python version must be Python 3.9 or higher (3.12 was used during development).

    • Check the available Python with python --version
    • If required, install or load a compatible python version. Your HPC administrator will be able to help with getting a compatible Python version.
    • then python -m venv <path-to-venv> with a path of your choosing.

  2. Source the new newly created python venv

    • source <path-to-venv>/bin/activate (Assuming you're using Bash or similar. Use the appropriate activate script within that folder depending on your shell)

  3. Clone this repository

    • Assuming you have already cloned this repository into a directory, move into the 'root' of this repository. cd polarroute-pipeline.
    • Otherwise git clone https://github.com/bas-amop/PolarRoute-pipeline.git polarroute-pipeline
    • then cd polarroute-pipeline

  4. Install requirements

    • Using python pip (inside the created venv) python -m pip install -r requirements.txt