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Make sure you have Python 3.9 installed along with pip. To check if they are installed, run:

python --version
pip --version

or, depending on you machine configuration:

python3 --version
pip3 --version

We will assume the commands' names are pip and python. Use pip3 and python3 if your machine is configured differently.

Docker or Singularity

Make sure you have the latest version of Docker or Singularity 3.10 installed.

To verify docker is installed, run:

docker --version

To verify singularity is installed, run:

singularity --version

If using Docker, make sure you can run Docker as a non-root user.

Install MedPerf

  1. (Optional) MedPerf is better to be installed in a virtual environment. We recommend using Anaconda. Having anaconda installed, create a virtual environment medperf-env with the following command:

    conda create -n medperf-env python=3.9

    Then, activate your environment:

    conda activate medperf-env
  2. Clone the MedPerf repository:

    git clone
    cd medperf
  3. Install MedPerf from source:

    pip install -e ./cli
  4. Verify the installation:

    medperf --version

What's Next?