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Snakemake Logger Plugin - Flowo

A Snakemake logger plugin designed to be used with FlowO for real-time task monitoring, making workflow management simple, interactive, and fun! 🎉

Demo page: flowo online

🎈 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

🔧 Configuration

# To generate the default configuration file, run the following command:
# This will create the default .env configuration file in your $HOME/.config/flowo/ directory.
flowo --generate-config

# After generating the .env file, open it with your preferred text editor to adjust the settings:
vim $HOME/.config/flowo/.env

The following environment variables are available for configuration in the .env file:

  • POSTGRES_USER: PostgreSQL username (default: flowo)
  • POSTGRES_PASSWORD: PostgreSQL password (default: flowo_password)
  • POSTGRES_DB: PostgreSQL database name (default: flowo_logs)
  • POSTGRES_HOST: PostgreSQL host (default: localhost)
  • POSTGRES_PORT: PostgreSQL port (default: localhost: 5432)
  • FLOWO_USER: User displayed in Flowo
  • FLOWO_WORKING_PATH: Snakemake execution project path

🚀 Usage

Basic usage

snakemake --logger flowo

config flowo_project_name or flowo_tags

snakemake \
    --config flowo_project_name=your_project_name flowo_tags="tagA,tagB,tagC" \
    --logger flowo

or config in --configfile

flowo_project_name: your_project_name
flowo_tags: "tagA,tagB,tagC"

🙏 Acknowledgement

This project is developed based on the excellent work of cademirch/snakemake-logger-plugin-snkmt. Special thanks to the original author for providing a solid foundation under the MIT License.