snakemake-logger-plugin-flowo 0.1.0

A Snakemake logger plugin that stores workflow execution data in PostgreSQL

Snakemake Logger Plugin - Flowo

A Snakemake logger plugin that stores workflow execution data in PostgreSQL.

Features

• Stores Snakemake workflow execution data in PostgreSQL database
• Tracks jobs, rules, files, and errors
• Provides comprehensive logging and monitoring capabilities
• Easy integration with existing Snakemake workflows

Installation

pip install snakemake-logger-plugin-flowo

Usage

1. Configure Database

Set up your PostgreSQL database and configure the connection:

export POSTGRES_USER=snakemake
export POSTGRES_PASSWORD=snakemake_password
export POSTGRES_DB=snakemake_logs

2. Use with Snakemake

Run your Snakemake workflow with the logger plugin:

snakemake --logger flowo

Configuration

The plugin can be configured using environment variables:

• POSTGRES_USER: PostgreSQL username (default: snakemake)
• POSTGRES_PASSWORD: PostgreSQL password (default: snakemake_password)
• POSTGRES_DB: PostgreSQL database name (default: snakemake_logs)
• SQL_ECHO: Enable SQL query logging (default: False)

Development

Setup

git clone <repository-url>
cd snakemake-logger-plugin-flowo
uv sync

Build

uv build

License

MIT License