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snkmt

(★ 67)

A TUI for monitoring Snakemake workflows in real-time.

File Explorer

Download Latest Version (.zip)

- - release-please.yml
  - test.yml
- - long-success.smk
  - simple-failure.smk
  - simple-success.smk
- run.sh
- - snkmt_logo_dark.svg
  - snkmt_logo_light.svg
- - dashboard.png
  - failedjob_dropdown.png
  - logfile_modal.png
  - workflow_failed.png
- - __init__.py
  - cli.py
  - py.typed
  - version.py
- - legacy.db
- __init__.py
- test_cli.py
- test_db.py
.gitattributes
.gitignore
CHANGELOG.md
LICENSE
pyproject.toml
README.md

# Installation Guide

1. Get the code

git clone https://github.com/cademirch/snkmt

Downloads the entire project code from GitHub to your computer.

cd snkmt

Moves into the project folder you just downloaded.

2. Official Install Script

Easy Recommended

Prerequisites

Python 3 Python is required to use pip.

pip install snakemake-logger-plugin-snkmt

Installs the package published on PyPI directly — no need to clone the source.

✅ After installing, open a new terminal and run the program's version command (e.g. --version) to confirm it worked.

Pulled directly from this repo's README.

3. Python

Easy

Prerequisites

Git Needed to download the project code from GitHub.
Python 3 On Windows, be sure to check 'Add Python to PATH' during installation.

pip install snakemake-logger-plugin-snkmt

Installs the package published on PyPI directly — no need to clone the source.

✅ If it runs without errors and prints output in the terminal, it worked.

Pulled directly from this repo's README.

// repository documentation

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<div align="center">
    <picture>
    <source media="(prefers-color-scheme: dark)" srcset="docs/logo/snkmt_logo_dark.svg">
    <source media="(prefers-color-scheme: light)" srcset="docs/logo/snkmt_logo_light.svg">
    <img alt="snkmt Logo" src="docs/logo/snkmt_logo_light.svg" width="350" height="auto">
    </picture>
</div>

## 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.

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

## 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):

```bash
pip install snakemake-logger-plugin-snkmt
```

This will automatically install snkmt as a dependency.

## Usage

### Execute a Snakemake workflow

```bash
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
- `r`: Force refresh tables
- `h`: Hide selected workflow
- `u`: Unhide all workflows
- `d`: Delete selected workflow
- `Ctrl+P`: Open database source selector
- `q` / `Ctrl+C`: Quit application

```bash
snkmt console
```

Options:
- `--db-path, -d`: Specify custom database path
- `--refresh-interval, -r`: Auto-refresh interval in seconds (default: 1.0, set to 0 to disable — useful for NFS or remote filesystems)

### Database Commands

View database information:
```bash
snkmt db info [DB_PATH]
```

Migrate database to latest version:
```bash
snkmt db migrate [DB_PATH]
```

## Configuration

By default, snkmt stores data in the [XDG Base Directory](https://specifications.freedesktop.org/basedir-spec/latest/) specified user data directory. You can customize this location using the `--db-path` option or by configuring the logger plugin.

## Screenshots

### Main Dashboard
<img src="docs/screenshots/dashboard.png" alt="snkmt dashboard showing workflow list and details" width="800">

### Error Inspection
<img src="docs/screenshots/failedjob_dropdown.png" alt="Error view showing failed jobs and log files" width="800">

<img src="docs/screenshots/logfile_modal.png" alt="Error view showing failed jobs and log files" width="800">

## License

This project is licensed under the MIT License. See the `LICENSE` file for details.