Installing EpiBenchmark on the UNC Longleaf Cluster¶

This guide describes how to install and use EpiBenchmark on the UNC Longleaf HPC cluster. If you only want to use EpiBenchmark on your machine, you need not do anything beyond the standard installation instructions.

Prerequisites¶

Before installing EpiBenchmark, verify or load a compatible Python module.

Verify the Python version:

python --version

List the available Python versions:

module avail python

Load a supported version (Python 3.10 or newer). For example:

module load python/3.11

Note The exact module name may change over time. Use module avail python to see the versions currently available on Longleaf.

Clone the repository:

git clone https://github.com/ACCIDDA/EpiBenchmark.git
cd EpiBenchmark

Option 1: Install with uv¶

First, verify whether uv is available:

uv --version

If uv is installed, create the virtual environment and install EpiBenchmark package:

uv sync

Activate the environment:

source .venv/bin/activate

Verify the installation:

epibench --help

If uv is not installed¶

Install uv into your user account:

python -m pip install --user uv

Make sure your user-level executable directory is on your PATH. Users can run echo $PATH to check user-level directory. If you see /nas/longleaf/home/<onyen_ID>/.local/bin in the output list, then your PATH is already configured correctly.

Then run:

uv sync

Verify the installation:

epibench --help

Option 2: Install with pip¶

Create a virtual environment:

python -m venv .venv

Activate it:

source .venv/bin/activate

Upgrade pip:

python -m pip install --upgrade pip

Install EpiBenchmark package:

python -m pip install -e .

Verify the installation:

epibench --help

Running EpiBenchmark¶

Activate the virtual environment whenever you begin a new session:

source .venv/bin/activate

Example commands:

epibench
epibench --help
epibench create --help
epibench score --help
epibench plot --help

Deactivate the environment when finished:

deactivate