snakemake-logger-plugin-flowo 2.0.1

A unified PostgreSQL-based logging plugin and backend for Snakemake

Flowo 🚀

Welcome to Flowo – your real-time Snakemake workflow dashboard!

Demo page: flowo online

Documentation: flowo docs

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✨ Features

• ⚡ Real-time Monitoring: Instant workflow updates via SSE.
• 🔐 Authentication: Secure JWT-based registration and login.
• 🚀 Efficient: Smart polling and debouncing for low network overhead.
• 🔍 Search & Filter: Find workflows by name, tags, or user.
• 🧩 Rule Focus: Filter jobs and update execution timeline by rule.
• 🖼️ Result Preview: Preview output files directly in the browser.
• 📋 Detailed Logs: Access comprehensive workflow and job logs.

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🛠️ Workflows

📊 Dashboard

🕹️ Jobs

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🚦 Installation

1️⃣ Install the Snakemake Logger Plugin

pip install snakemake-logger-plugin-flowo

The PyPI package does not depend on Snakemake itself (it is expected in the environment where you run workflows). If you need Snakemake installed in the same environment—for example a minimal venv used only for the CLI—use:

pip install "snakemake-logger-plugin-flowo[snakemake]"

2️⃣ Install the Flowo web server (Single Image)

This method uses pre-built Docker images. For detailed instructions, please refer to the Quick Start guide.

Clone the repo and start the service:

git clone https://github.com/zhanghaomiao/flowo.git
cd flowo
cp env.example .env
# Edit .env:
# - set SECRET_KEY to a long random value and keep it stable
# - set FLOWO_WORKING_PATH to a host directory for FlowO data
docker compose up -d

Open http://localhost:3100 to create your account.

Generate a token in your profile settings to configure the logger plugin.

Copy and run the CLI config snippet from the dashboard to finish setup.

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🚀 Usage

cd /path/to/flowo_project_dir
mkdir demo                # Create a demo project folder
cd demo
wget https://raw.githubusercontent.com/zhanghaomiao/flowo/refs/heads/main/tests/demos/Snakefile
# Run snakemake with flowo logger
snakemake \
    --logger flowo \
    --logger-flowo-name=your_project_name \
    --logger-flowo-tags="tagA,tagB,tagC"

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👩‍💻 Developer Guide

If you want to contribute or build from source:

docker compose -f compose.dev.yml up --build

• Gateway: http://localhost:3100 (Accesses both Frontend and Backend)
• Backend API: http://localhost:8000
• Frontend: http://localhost:5173