Installation

pixy is available for Linux and macOS. For a guided walkthrough — including generating an AllSites VCF, filtering it, and running your first analysis — see Step by Step Installation and Usage. The instructions below are the minimal copy-pasteable version for users who already know what they're doing.

Via conda

We recommend installing into a fresh conda environment. If you don't already have a conda distribution installed, we recommend Miniforge (lightweight, fully free, conda-forge pre-configured, ships with the fast mamba solver) or Miniconda. The full Anaconda distribution also works but has more restrictive licensing for commercial or large-organization use.

pixy supports Python 3.9–3.11 (3.12 is not yet supported):

conda create -n "pixy" python=3.11
conda activate pixy
conda install -c conda-forge pixy
conda install -c bioconda samtools

(The samtools install pulls in htslib as a dependency, which provides the bgzip and tabix utilities you'll need to prepare your VCF.)

Test the installation by running:

pixy --help

Note

If the conda solver hangs on environment creation, install mamba and use it in place of conda for the install steps (mamba install ...). Miniforge ships with mamba already, and recent conda releases support --solver=libmamba for the same speedup.

From source

To work from the latest code (or to contribute), clone the repository and install in editable mode. pixy uses Poetry for dependency management:

git clone https://github.com/ksamuk/pixy.git
cd pixy
poetry install
poetry run pixy --help

If you'd rather not install Poetry, you can install the package with pip into an existing environment:

git clone https://github.com/ksamuk/pixy.git
cd pixy
pip install -e .

In either case you'll still need bgzip and tabix on your PATH (install samtools from bioconda, or your distribution's package manager, to get them).