Installation

Requirements

wisp requires Python 3.11 or 3.12. Runtime command line tools depend on the input mode:

• BAM/CRAM mode requires samtools, mosdepth, bedtools, bgzip, and tabix.

• All-sites VCF mode requires bgzip and tabix.

The repository environment file installs these external tools from conda-forge and bioconda.

Conda environment

From the repository root, create and activate the development environment:

mamba env create -f environment.yml
conda activate wisp
python -m pip install -e ".[dev]"

If the environment already exists, update it instead:

mamba env update -n wisp -f environment.yml
conda activate wisp
python -m pip install -e ".[dev]"

Verify the CLI

After installation, verify the wisp command:

wisp --help
wisp --version

Build these docs locally

Install the docs dependencies and build the HTML documentation:

python -m pip install -e ".[docs]"
make -C docs html

The rendered site is written to docs/_build/html/index.html.