snkmt 0.1.2

Realtime monitoring of Snakemake workflows

snkmt

A CLI utility for monitoring running Snakemake workflows in real-time.

Note: This project is still under active development. Please report bugs, weird UI behavior, and feature requests - they are greatly appreciated!

Overview

snkmt (Snakemate) works with the snakemake-logger-plugin-snkmt plugin to capture and store Snakemake workflow execution data in a SQLite database. This allows you to monitor workflow progress, view job statuses, and troubleshoot errors through an interactive terminal interface.

How it Works

1. The snakemake-logger-plugin-snkmt plugin captures workflow events during Snakemake execution
2. Events are written to a local SQLite database
3. snkmt provides tools to view and monitor this data through a terminal UI and CLI commands

Installation

Install via the logger plugin (recommended):

pip install snakemake-logger-plugin-snkmt

This will automatically install snkmt as a dependency.

Usage

Execute a Snakemake workflow

snakemake --logger snkmt ...

Interactive Console

Launch the real-time monitoring interface:

• Tab / Shift+Tab: Navigate between interface elements
• Enter: Select workflow rows or log files
• Escape: Close modals/dialogs
• q / Ctrl+C: Quit application

snkmt console

Options:

• --db-path, -d: Specify custom database path

Database Commands

View database information:

snkmt db info [DB_PATH]

Migrate database to latest version:

snkmt db migrate [DB_PATH]

Configuration

By default, snkmt stores data in the XDG Base Directory specified user data directory. You can customize this location using the --db-path option or by configuring the logger plugin.

Screenshots

Main Dashboard

Error Inspection