User Guide

Everything you need to install Bio_pype, configure it for your system, pull workflows from the registry, and run them — without writing any pipeline code yourself.

If you instead want to author snippets, pipelines and profiles, see the Developer Guide.

Getting started

• About
  • Snippets
  • Pipelines
  • Profiles
  • Registry
• Getting Started
  • Requirements
  • Installation
  • Quick Start: Using Workflows from the Registry
  • Manual Setup (Advanced)
• Configuration
  • Configuration Overview
  • Module Paths
  • Configuration Methods
  • Configuration Variables
  • Compute.bio API Integration

Running workflows

• Workflow Registry
  • Concepts
  • Getting Started
  • Managing Installed Workflows
  • Publishing Workflows
  • Configuration
• Quick Start
• Concepts
  • Template Paths
  • Template Arguments
  • Template Variables
  • Directory Creation
• Complete Example
• Command-line Options
• Comparison with pype pipelines
• Advanced Features
  • Argument Types
  • Nested Pipelines
• Troubleshooting
• See Also
• Profiles
  • Profile Structure
  • Section Details
  • Namespace Types
  • Understanding Dependencies
  • Complete Profile Examples
  • Using Profiles in Snippets
  • Best Practices
  • Troubleshooting
  • Reference
  • Profile CLI Commands
  • Building Profiles Automatically
  • Additional Resources
• Queue Systems
  • Overview
  • Available Queue Systems
  • Resource Requirements
  • Job Dependencies
  • Job Submission and Monitoring
  • Custom Queue Adapters
  • Best Practices
  • Troubleshooting
  • Integration with Progress Tracking
  • See Also

Monitoring & sustainability

• Progress Tracking
  • Overview
  • Core Classes
  • Display Modes
  • Pipeline Runtime Tracking
  • Compute.bio API Integration
  • Integration with Pipelines
  • See Also
• Pipeline Resume
  • Overview
  • How Resume Works
  • Command Line Usage
  • Command Line Options
  • Environment Restoration
  • Usage Examples
  • Queue System Integration
  • Inspecting Runtime Files
  • Troubleshooting
  • Best Practices
  • See Also
• Understanding Bio_pype Logs
  • Log Structure
  • Log File Types
  • Useful Log Commands
  • Debug Tips
  • Common Issues
• Energy and Carbon Tracking
  • What you get
  • Enabling carbon tracking
  • Carbon intensity providers
  • Intensity caching
  • The power model
  • Green-window scheduling
  • Configuration reference