Quick Start#

This page shows the fastest way to start OntoAnno for your dataset.

Get OntoAnno#

First, clone the OntoAnno repository:

git clone https://github.com/tamuya23/OntoAnno.git
cd OntoAnno

Choose Installation Method#

Setup

Use this when

Main command

Docker

You are on a laptop, workstation, or Linux server with Docker.

./scripts/start_ontoanno_docker.sh

Apptainer

You are on an HPC system where Docker is not allowed.

./scripts/start_ontoanno_apptainer.sh

Install Docker if Needed#

If docker --version fails, install Docker before using the Docker setup.

  • On a laptop or workstation, install Docker Desktop.

  • On a Linux server where you have admin access, install Docker Engine.

  • On HPC systems where Docker is not available or not allowed, use the Apptainer setup instead.

After installation, check:

docker --version
docker compose version

Docker Setup#

Use Docker if you are on your own computer or a regular server.

  1. Prepare folders and set your API key in the terminal:

    bash scripts/docker_setup.sh
export OPENAI_API_KEY=your_api_key_here

  2. Put your data files in data/. Then configure configs/demo.yaml using Data Configure.

  3. Start OntoAnno:

    ./scripts/start_ontoanno_docker.sh configs/demo.yaml

Apptainer Setup#

Use Apptainer on HPC systems such as Longleaf.

  1. Prepare folders and set your API key in the terminal:

    bash scripts/apptainer_setup.sh
export OPENAI_API_KEY=your_api_key_here

  2. Put your data files in data/. Then configure configs/demo.yaml using Data Configure.

  3. Start OntoAnno:

    ./scripts/start_ontoanno_apptainer.sh configs/demo.yaml

Open the Web App#

After starting OntoAnno with Docker or Apptainer, open the URL printed in the terminal, usually http://127.0.0.1:8501.

If you are connected through SSH or HPC, use VS Code port forwarding or forward port 8501 manually.

After installation, follow Agent Guide to annotate a new Seurat dataset.