BIO Pype

A lightweight python framework to organize bioinformatics scripts and analyses.

Getting Started

• About
  • Snippets
  • Pipelines
  • Profiles
• Getting Started
  • Requirements
  • Installation
  • Basic Setup
  • First Steps
• Configuration
  • Configuration Overview
  • Module Paths
  • Configuration Methods
  • Environment Configuration
  • Configuration Variables
• Available modules:
  • Browse and install available modules

Core Components

• Snippets
  • Basic Snippet Structure
  • Reference arguments results and files
  • Using Namespaces
  • Advanced Snippets in Python
• Pipelines
  • Pipeline Structure
  • Info Section
  • Pipeline Items
  • Resource Management
  • Running Pipelines
  • Complete Example
• Profiles
  • Profile Configuration
  • Profile Structure
  • Example Profiles

Usage & Troubleshooting

• Understanding Bio_pype Logs
  • Log Structure
  • Log File Types
  • Useful Log Commands
  • Debug Tips
  • Common Issues
• API Documentation
  • pype.utils
  • pype.process
  • pype.misc
  • pype.logger
  • pype.exceptions
  • Core Components
  • Utilities

Indexes and tables

• Index

• Module Index

• Search Page