Installation

Via Bioconda

mamba install -c conda-forge -c bioconda wasp2

Bioconda installs WASP2 together with the external command-line dependencies required by the workflows, including samtools, bcftools, and bedtools.

Via PyPI

pip install wasp2

The PyPI wheel includes the WASP2 Python package and Rust extension, but it does not install external tools such as samtools, bcftools, or bedtools. Install those separately before running mapping or counting.

Via Docker

The Docker image is the most reproducible fully bundled option available in this environment.

docker pull ghcr.io/mcvickerlab/wasp2:1.4.0

docker run --rm ghcr.io/mcvickerlab/wasp2:1.4.0 wasp2-count --help
docker run --rm ghcr.io/mcvickerlab/wasp2:1.4.0 wasp2-map --help
docker run --rm ghcr.io/mcvickerlab/wasp2:1.4.0 wasp2-analyze --help
docker run --rm ghcr.io/mcvickerlab/wasp2:1.4.0 wasp2-ipscore --help

Via Singularity/Apptainer

For HPC environments that require SIF images:

singularity pull wasp2.sif docker://ghcr.io/mcvickerlab/wasp2:1.4.0
singularity exec wasp2.sif wasp2-count --help

or with Apptainer:

apptainer pull wasp2.sif docker://ghcr.io/mcvickerlab/wasp2:1.4.0
apptainer exec wasp2.sif wasp2-count --help

Note

Docker was validated in this development environment. apptainer / singularity binaries were not available locally during this doc update, so those examples reflect the intended pull/exec workflow but were not executed here.

Development Installation

git clone https://github.com/mcvickerlab/WASP2.git
cd WASP2
pixi install
pixi run verify

Verification

wasp2-count --help
wasp2-map --help
wasp2-analyze --help
wasp2-ipscore --help