Installation¶

Choose the installation method that fits your use case:

CLI — install with pip, Bioconda, or from source
Web app — run with Docker or from source

CLI installation¶

via pip¶

git clone https://github.com/the-foxlab/ResistanceProfiler.git
cd ResistanceProfiler
pip install -e ".[dev]"
respro --version

via Bioconda¶

conda create -n respro -c conda-forge -c bioconda respro
conda activate respro
respro --version

Bioconda is the recommended install path if you already use conda/mamba — it handles the mappy native dependency automatically without a C compiler.

via BioContainers (Docker)¶

docker pull quay.io/biocontainers/respro

The BioContainers image provides a containerized CLI environment. Mount your data directories and run respro commands inside the container.

Web app¶

Docker (recommended)¶

Clone the repository and start the stack:

git clone https://github.com/the-foxlab/ResistanceProfiler.git
cd ResistanceProfiler
docker compose -f docker-compose.web.yml up --build

Or pull the released image directly. The image is published as a Docker image on GitHub Container Registry:

docker pull ghcr.io/the-foxlab/resistanceprofiler:latest

The stack includes the FastAPI backend, an RQ worker, and Redis. Open the app at http://127.0.0.1:8000/. For configuration options (authentication, CORS, rate limiting, data directories), see Web app.

Next steps

After installation, continue to Quickstart or Database Preparation.