snakemake-logger-plugin-flowo 2.0.4

A unified PostgreSQL-based logging plugin and backend for Snakemake

FlowO

FlowO is a Snakemake observability and workflow catalog platform: run the official logger plugin alongside Snakemake, and the web app records every execution—live Dashboard and Runs, job-level logs and errors, optional output preview, and a catalog of versioned Snakemake projects you can browse, edit, and link back to runs.

Full documentation: flowo-docs.pages.dev

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Why FlowO

Real-time run monitoring	PostgreSQL-backed history with SSE so the Dashboard and Runs views update as jobs start, finish, or fail.
Deep visibility	Per-run DAG, Jobs, Timeline, captured code, and logs—plus result preview when the server can read the same paths Snakemake used.
Workflow catalog	The Catalog stores Snakemake templates in the database (with versioning), materializes a workspace for Snakemake/DAG tooling, and ties runs to catalog entries when you report catalog metadata from the logger.

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Quick start (~5 minutes)

1. Run FlowO (Docker Compose, .env, FLOWO_WORKING_PATH) — follow Quick Start in the docs.

2. Install the logger plugin on the machine where Snakemake runs:

   pip install snakemake-logger-plugin-flowo
   

   Optional: pip install "snakemake-logger-plugin-flowo[snakemake]" if you need Snakemake in the same venv.

3. Authenticate the CLI (browser flow; token is written to ~/.config/flowo/config.toml, mode 0600):

   flowo login --host http://localhost:3100
   

   Replace the URL with your deployment (HTTPS in production).

4. Run Snakemake with the FlowO logger and open Dashboard / Runs in the browser:

   cd /path/to/your/workflow
   snakemake --logger flowo \
     --logger-flowo-name "my-run" \
     --logger-flowo-tags "demo,qc"
   

Headless servers, CI, or MCP: create a long-lived token under Settings → API Tokens only when you cannot use flowo login. See Login and CLI setup (manual token section).

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Screenshots

Dashboard — fleet status and activity	Run detail — DAG, jobs, timeline, code, results

Catalog — browse stored workflows	DAG preview — best-effort rule graph (catalog / template)

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Documentation map

Section	What you will find
Quick Start	Shortest path: Compose, flowo login, first Snakemake run.
User manual (same site)	Installation, Runs, catalog, DAG preview, results, jobs & errors.
Architecture	Data flow, catalog storage model.
Advanced features	Optional MCP and email (SMTP); not required for core use.

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Contributing & development

git clone https://github.com/zhanghaomiao/flowo.git
cd flowo
docker compose -f compose.dev.yml up --build

• Gateway: http://localhost:3100 (combined frontend + API in dev compose)
• Backend API: http://localhost:8000
• Frontend (Vite): http://localhost:5173

Build the docs locally:

uv sync --extra docs
uv run mkdocs build --strict

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Live demo

A hosted sandbox may be available at flowo.iregene-bio.com. For credentials or access policy, see the Quick Start or contact the maintainers.