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Quick Start

Docker Compose → sign in → flowo login → one Snakemake run with --logger flowo, then check Dashboard / Runs.

If FlowO is already running elsewhere, use that URL instead of http://localhost:3100 and skip Deploy.

Install FlowO with Docker Compose

Deploy

  1. Fetch configuration (adjust if you mirror the repo):
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

  1. Edit .env — set FLOWO_WORKING_PATH, SECRET_KEY, and DB passwords at minimum; optionally FLOWO_BOOTSTRAP_ADMIN_EMAIL / FLOWO_BOOTSTRAP_ADMIN_PASSWORD, DOMAIN / FLOWO_HOST. Remove bootstrap password from .env after you can sign in.

  2. Start

docker compose up -d

Superuser

Superuser

If FLOWO_BOOTSTRAP_ADMIN_EMAIL and FLOWO_BOOTSTRAP_ADMIN_PASSWORD are set in .env, the first start already created a superuser (see Edit .env above). Otherwise run:

docker compose exec flowo python -m app.manage create-admin you@example.com 'your-strong-password'

Open http://localhost:3100, sign in, and register another user from the login page if public signup is enabled.

Logger and CLI

pip install snakemake-logger-plugin-flowo
flowo login --host http://localhost:3100

Complete the browser approval; the CLI writes ~/.config/flowo/config.toml (mode 0600). You should see something like Login successful. Configuration saved to ~/.config/flowo/config.toml.

First Snakemake run

Work under the host directory you set as FLOWO_WORKING_PATH in .env (same tree the server mounts) so Result preview matches reported paths.

cd /path/to/FLOWO_WORKING_PATH
flowo catalog new flowo-quickstart
cd flowo-quickstart
flowo catalog upload --path .
snakemake -n --cores 1 --directory .test --logger flowo \
  --logger-flowo-name "Quickstart" \
  --logger-flowo-tags "demo" \
  --logger-flowo-catalog flowo-quickstart

Omit flowo catalog upload if you only want a run without a catalog link. Template layout, uploads, and logger flags in depth: Catalog and templates, Run Snakemake with FlowO.

Then open Runs (and Dashboard) for the new run.

Next steps