Installation

vcfsim is available for Linux and macOS. The instructions below cover the standard conda install, plus an editable install from source for development.

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:

conda create -n vcfsim_env python=3.10
conda activate vcfsim_env
conda install -c bioconda vcfsim

Test the installation by running:

vcfsim --help

For the full bioconda recipe and release history see https://bioconda.github.io/recipes/vcfsim/README.html.

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 with pip:

git clone https://github.com/samuk-lab/vcfsim.git
cd vcfsim
pip install -e .
vcfsim --help

This pulls in the runtime dependencies — numpy, msprime, and tskit — automatically. We recommend doing this inside a fresh conda environment to keep the msprime build dependencies isolated from your system Python.