Snakemon - Snakemake Monitor

Snakemon is a lightweight web service designed to monitor the execution of Snakemake workflows, specifically targeting versions using the legacy WMS monitoring protocol (generally prior to v9.x).

It listens for HTTP requests sent by Snakemake when configured with the --wms-monitor flag found in those older versions, logs workflow events to a database, and attempts to determine the final status (success or error) of the workflow.

Purpose

  • Provide a persistent record of Snakemake workflow runs.

  • Offer a simple API compatible with the legacy --wms-monitor feature.

  • Store workflow details (ID, start/end times, status) and logs in a configurable database (SQLite or PostgreSQL).

Features

  • Workflow Tracking: Monitor and persist the progress of Snakemake workflows.

  • Status Detection: Automatically determine workflow success or error status.

  • Log Collection: Store and view all log messages generated during workflow execution.

  • Web Interface: Access workflow information through a simple web UI.

  • Flexible Database Support: Use SQLite for development or PostgreSQL for production environments.

  • Docker Support: Deploy easily using Docker containers for both backend API and frontend UI.

Architecture

Snakemon consists of two main components:

  1. Backend API Service: * FastAPI-based REST API that receives and processes Snakemake monitoring events * SQLAlchemy ORM for database operations * Provides endpoints for creating and updating workflow status

  2. Frontend Web Interface: * React-based single-page application * View workflows and their details, including logs and execution status * Simple, responsive UI for monitoring workflow progress

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