Installation#

Requirements#

System Dependencies#

WASP2 requires:

  • bcftools >= 1.10

  • bedtools >= 2.29

  • samtools >= 1.10

On Ubuntu/Debian:

sudo apt-get install bcftools bedtools samtools

On macOS with Homebrew:

brew install bcftools bedtools samtools

Python Requirements#

  • Python >= 3.10

  • See pyproject.toml for full list

Installation#

Development Installation#

git clone https://github.com/Jaureguy760/WASP2-final.git
cd WASP2-final
pip install -e ".[dev]"

Conda Installation#

conda env create -f environment.yml
conda activate wasp2

Docker Installation#

WASP2 is available as a Docker image with all dependencies pre-installed. This is the easiest way to get started, especially on systems where installing bioinformatics tools is challenging.

Pull from GitHub Container Registry:

docker pull ghcr.io/jaureguy760/wasp2-final:latest

Run WASP2 commands:

# Run counting
docker run -v /path/to/data:/data ghcr.io/jaureguy760/wasp2-final:latest \
    wasp2-count count-variants /data/sample.bam /data/variants.vcf

# Interactive shell
docker run -it -v /path/to/data:/data ghcr.io/jaureguy760/wasp2-final:latest bash

Build locally (optional):

git clone https://github.com/Jaureguy760/WASP2-final
cd WASP2-final
docker build -t wasp2:local .

For detailed Docker usage including GPU support and Singularity conversion, see the Container Usage Guide.

Singularity/Apptainer#

For HPC environments that don’t support Docker, use Singularity/Apptainer:

# Pull from GitHub Container Registry
singularity pull wasp2.sif docker://ghcr.io/jaureguy760/wasp2-final:latest

# Run WASP2 commands
singularity exec wasp2.sif wasp2-count --help

# Build from definition file
singularity build wasp2.sif Singularity.def

Verification#

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