Installation¶

Prerequisites¶

VNtyper 2 requires the following to be installed on your system:

Dependency	Minimum Version	Purpose
Python	3.9+	Core runtime
Java	11+	Kestrel genotyping engine
BWA	0.7.18+	Read alignment
samtools	1.20+	BAM/CRAM manipulation
fastp	0.23+	FASTQ quality control

External tools required

External tools (BWA, samtools, fastp, Java 11) must be installed separately when using pip or source installation. The Docker image includes all dependencies.

Install VNtyper 2¶

pipFrom SourceCondaDocker

Install directly from GitHub:

pip install git+https://github.com/hassansaei/VNtyper.git

Clone the repository and install in editable mode:

git clone https://github.com/hassansaei/vntyper.git
cd vntyper
pip install -e .

Use the provided environment file to create a Conda environment with all dependencies (including external tools):

git clone https://github.com/hassansaei/vntyper.git
cd vntyper

# Create the environment
conda env create -f conda/environment_vntyper.yml
conda activate vntyper

# Install VNtyper 2 into the environment
pip install -e .

The environment_vntyper.yml includes Python 3.9, BWA, samtools, fastp, OpenJDK 11, and all Python dependencies.

Additional environment files are available for optional modules:

conda/environment_envadvntr.yml --- adVNTR genotyping module
conda/environment_shark.yml --- SHARK read filtering module

Pull the pre-built image from Docker Hub or GitHub Container Registry:

# Docker Hub
docker pull saei/vntyper:latest

# GitHub Container Registry
docker pull ghcr.io/hassansaei/vntyper:latest

Or build from source:

git clone https://github.com/hassansaei/VNtyper.git
cd VNtyper
DOCKER_BUILDKIT=1 docker build -f docker/Dockerfile -t vntyper:latest .

Verify Installation¶

Confirm VNtyper 2 is installed correctly:

vntyper --version

Development Install¶

To install with development dependencies (Ruff linter, pytest, mypy):

git clone https://github.com/hassansaei/vntyper.git
cd vntyper
pip install -e .[dev]

Run the test suite to verify everything works:

make test-unit

See the Contributing Guide for full development setup instructions.