snakemake-logger-plugin-flowo 2.1.0

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

---

Live demo

A hosted sandbox may be available at flowo.iregene-bio.com.

• Email: [e-mail]
• Password: demo1234

For credentials or access policy, see the Quick Start or contact the maintainers.

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.

---

Quick start (~10 minutes)

1. Deploy with Docker Compose

From an empty directory (or use the same files from a git clone of this repo instead of curl):

curl -O https://raw.githubusercontent.com/zhanghaomiao/flowo/main/compose.yml
curl -O https://raw.githubusercontent.com/zhanghaomiao/flowo/main/env.example
cp env.example .env

Edit .env: set FLOWO_WORKING_PATH to a host path that contains (or is a parent of) your Snakemake project directories so logs and file previews resolve; set SECRET_KEY (and database passwords) for anything beyond a local trial.

Start the stack (PostgreSQL + FlowO image on port 3100 by default):

docker compose up -d

Wait until the flowo container is healthy, then continue.

More detail (HTTPS, UID/GID, paths, all env vars): Installation, Environment variables, and Quick Start.

2. Create an administrator (superuser)

Web self-registration creates a normal user. For Settings, user administration, invitations when public signup is off, and similar capabilities, you need at least one superuser. Pick one of these:

A — Environment variables (best for people who only pull compose.yml / image): in .env set both (example values are placeholders only):

FLOWO_BOOTSTRAP_ADMIN_EMAIL=[e-mail]
FLOWO_BOOTSTRAP_ADMIN_PASSWORD='your-strong-password'

Then docker compose up -d as usual. On first start, after migrations, the container creates that superuser only if the database has no superuser yet. Remove or blank these variables after the first successful deploy; do not keep bootstrap passwords in .env long term. This path applies to the published Docker image whose entrypoint runs migrations and bootstrap (the default compose.yml). If you start the API from source without that entrypoint (for example compose.dev.yml), use option B or run python -m app.manage bootstrap-admin-from-env once with the same environment variables and database URL.

B — One command after the stack is up:

docker compose exec flowo python -m app.manage create-admin [e-mail] 'your-strong-password'

Use a dedicated admin email; you can still register or invite other users later. If you already cloned the repo and run Compose from the project root, the service name remains flowo. For compose.dev.yml, run the same command against the API container: docker compose -f compose.dev.yml exec flowo-backend python -m app.manage create-admin ….

3. Sign in and use the CLI logger

1. Open http://localhost:3100 (or your FLOWO_HOST) and sign in with the superuser from step 2 (bootstrap env or create-admin). If public registration is enabled, you can instead register a first user in the UI—use a superuser anyway when you need admin features.

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 and write ~/.config/flowo/config.toml with FLOWO_HOST, FLOWO_USER_TOKEN, and FLOWO_WORKING_PATH. Avoid passing tokens on the command line because they can leak through shell history, process listings, scheduler logs, or CI logs. See Login and CLI setup.

---

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)

---

Documentation map

Section	What you will find
Quick Start	Compose deploy, create-admin, flowo login, first Snakemake run.
Installation	Short Docker + .env checklist.
Environment variables	Full tables for Compose / server settings.
User manual (same site)	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.

---

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

---