BIO Pype

A lightweight python framework to organize bioinformatics scripts and analyses.

• About
• Get started
  • Requirements
  • Installation
  • Running tasks in a Snippet
• Configuration
  • Local configuration file
  • Environment variable
  • Available variables
• Available modules:
  • Browse and install available modules
• Snippets
  • Basic Snippet Structure
  • Reference arguments results and files
  • Using Namespaces
  • Advanced Snippets in Python
• Pipelines
  • Structure of Pipelines files:
  • Pipeline Item Arguments
• Profiles
  • Extending profiles:
• API
  • Utils
  • Process
  • Misc
  • Logging/Exceptions

Indexes and tables

• Index
• Module Index
• Search Page