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Installation

This page explains how to install PhEval and verify that it is available on your system.
Tool-specific execution details are handled by plugins and documented in their respective repositories.

Prerequisites

Before installing PhEval, ensure you have:

  • Python 3.10 or newer
  • A working Python environment (virtualenv, conda, uv, or similar)
  • pip or a compatible Python package manager

It is strongly recommended to install PhEval in an isolated environment.

Using venv:

python -m venv pheval-env
source pheval-env/bin/activate

On macOS/Linux, you should now see your environment name in the shell prompt.

Install PhEval

Install the latest released version from PyPI:

pip install pheval

This installs:

  • The PhEval command-line interface
  • The pheval-utils command-line utilities
  • Shared utilities used by plugins and runners

Verify the installation

Check that PhEval is installed correctly:

pheval --help

You should see output similar to:

Usage: pheval [OPTIONS] COMMAND [ARGS]...

Options:
  --help  Show this message and exit.

Commands:
  run     Execute a phenotype-driven tool via a runner
  update  Download or update required mapping resources

Verify that the utility commands are also available:

pheval-utils --help

You should see a list of available utility commands, including data preparation and benchmarking.

If either command is not found, ensure your virtual environment is activated.

Install a plugin

PhEval does not execute tools directly. Instead, plugins provide runners that implement tool-specific preparation, execution, and post-processing.

After installing PhEval, install one or more plugins corresponding to the tools you want to evaluate.

Each plugin:

  • Documents its own installation requirements
  • Exposes one or more runners
  • Explains how to invoke those runners using pheval run

See the Plugins section for a list of available plugins and links to their documentation.

Some workflows require up-to-date ontology and identifier mappings.

You can download or refresh these resources using:

pheval update

This step is recommended before running benchmarks, particularly when working with gene or disease identifiers.

Next steps

Once PhEval is installed: