biobuntu 0.1.0

Bioinformatics platform

BioBuntu

A comprehensive bioinformatics platform for running pipelines, with CLI, GUI, and web interfaces.

🚀 Features

• Project Management: Create and manage bioinformatics projects with organized directory structures
• Advanced Pipelines: Support for complex workflows with dependencies and parallel execution
• Multiple Interfaces: CLI, Desktop GUI (BioBuntu Studio), and Web Dashboard
• Remote Lab Support: API endpoints for remote pipeline execution with job tracking
• Packaging: Available as .deb packages, PPA, and Conda packages
• Workflow Support: RNA-seq, variant calling, metagenomics, and QC pipelines
• Tool Integration: Wrappers for FastQC, BWA, GATK, HISAT2, Samtools

📦 Installation

From Source

git clone https://github.com/GenomeHouse/biobuntu.git
cd biobuntu
pip install -e .

Debian/Ubuntu (.deb)

sudo dpkg -i biobuntu_0.1.0_all.deb
sudo apt-get install -f  # Install dependencies

Ubuntu PPA

sudo add-apt-repository ppa:genomehouse/biobuntu
sudo apt-get update
sudo apt-get install biobuntu

Conda

conda install -c genomehouse biobuntu

🏁 Quick Start

1. Create a project:

   biobuntu create-project myproject --description "RNA-seq analysis"
   

2. Run a pipeline:

   biobuntu run workflows/rnaseq.yaml --project myproject --input sample.fastq
   

3. Start web interface:

   biobuntu web
   

   Open: http://localhost:5000

💻 Usage

CLI Commands

BioBuntu provides a comprehensive CLI with 8 commands:

biobuntu --help                    # Show all commands
biobuntu create-project <name>     # Create new project
biobuntu list-projects             # List all projects
biobuntu delete-project <name>     # Delete project
biobuntu list                      # List workflows
biobuntu validate <workflow>       # Validate workflow
biobuntu run <workflow> [options]  # Run pipeline
biobuntu web                       # Start web dashboard
biobuntu gui                       # Start GUI application

Web Dashboard

Access the web interface at http://localhost:5000 with features:

• Create and manage projects
• Run pipelines locally or remotely
• Monitor remote jobs with real-time updates
• Download results and intermediate files

GUI Application

Launch BioBuntu Studio with biobuntu gui featuring:

• Project selection and creation
• Drag-and-drop file input
• Real-time progress tracking
• Workflow validation

📁 Project Structure

Projects are automatically organized:

~/biobuntu/projects/myproject/
├── raw_data/     # Input files
├── qc/          # Quality control results
├── processed/   # Intermediate processing files
├── results/     # Final analysis results
├── reports/     # Summary reports
├── logs/        # Execution logs
└── config/      # Project configuration

🔬 Advanced Pipelines

Features

• Dependencies: Steps can depend on previous steps
• Parallel Execution: Independent steps run concurrently
• Parameterization: Configurable tool arguments
• Validation: Check workflow structure before execution

Example Workflow

name: RNA-seq Pipeline
description: Complete RNA-seq analysis
steps:
  - name: qc
    tool: fastqc
    args:
      input_file: raw_data/sample.fastq
      output_dir: qc/
  - name: align
    tool: hisat2
    depends_on: [qc]
    args:
      index: genome_index
      input_fastq1: raw_data/sample.fastq
      output_sam: processed/sample.sam

🌐 Remote Lab Support

API Endpoints

• POST /api/remote/run - Submit remote jobs
• GET /api/remote/status/<job_id> - Check job status
• GET /api/remote/jobs - List all remote jobs
• Webhook callbacks for job completion

Example Remote Execution

import requests

# Submit job
response = requests.post('http://localhost:5000/api/remote/run', json={
    'workflow': 'rnaseq.yaml',
    'project': 'myproject',
    'callback_url': 'https://myapp.com/webhook'
})

job_id = response.json()['job_id']

📚 Documentation

• Getting Started - Quick start guide
• Pipelines - Pipeline creation and management
• GUI Guide - Desktop application usage
• Web Dashboard - Web interface documentation
• API Reference - Complete API documentation
• Development - Contributing and development guide

🛠️ Development

Prerequisites

• Python 3.8+
• Bioinformatics tools (optional, for testing)

Setup

git clone https://github.com/GenomeHouse/biobuntu.git
cd biobuntu
pip install -e .
pip install pytest black flake8  # Development dependencies

Testing

pytest                    # Run tests
black .                  # Format code
flake8 .                 # Check style

Building Packages

./scripts/build_deb.sh    # Debian package
./scripts/build_ppa.sh    # PPA package
./scripts/build_conda.sh  # Conda package

🤝 Contributing

We welcome contributions! Please see our Development Guide for details.

1. Fork the repository
2. Create a feature branch
3. Make your changes
4. Add tests
5. Submit a pull request

📄 License

This project is licensed under the MIT License - see the LICENSE file for details.

🙏 Acknowledgments

• Built with Python, Flask, Click, and tkinter
• Inspired by bioinformatics community needs
• Thanks to all contributors and users

📞 Support

• Issues: GitHub Issues
• Discussions: GitHub Discussions
• Documentation: Full Docs

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BioBuntu - Making bioinformatics accessible through modern interfaces and powerful automation.