installation.md

Installation

We recommend using Anaconda to install Harpy, and we provide an environment.yml.

1. Create the conda environment:

# Use standard Conda environment creation
conda env create -f environment.yml
# Or use Mamba as alternative
mamba env update -f environment.yml --prune

conda activate harpy

If you plan to use the Harpy function harpy.im.tiling_correction, please install jax and basicpy. On Mac and Linux, this can be done via pip install ..., on Windows you will have to run the following commands:

pip install "jax[cpu]" -f https://whls.blob.core.windows.net/unstable/index.html --use-deprecated legacy-resolver
pip install basicpy

On Mac, please comment out the line mkl=2024.0.0 in environment.yml.

For a mimimal list of requirements for Harpy, we refer to the setup.cfg.

2. Install Harpy:

pip install git+https://github.com/saeyslab/harpy.git

Additional dependencies

To use the plugin, run

pip install "git+https://github.com/saeyslab/harpy.git#egg=harpy[plugin]"

To run Harpy from the cli:

pip install "git+https://github.com/saeyslab/harpy.git#egg=harpy[cli]"

To be able to run the unit tests:

pip install "git+https://github.com/saeyslab/harpy.git#egg=harpy[testing]"

NVIDIA GPU support

We provide environment_vib_compute.yml that will install torch with NVIDIA GPU support on Linux (tested on CentOS). After creation of the environment via conda env create -f environment_vib_compute.yml, activate the environment, and install Harpy via pip install git+https://github.com/saeyslab/harpy.git.

For VIB members we also refer to this document, for an example on how to use the VIB compute cluster with GPU support.