User Guide

This is a general user guide. It will serve as an overview of the pipeline's structure, tools, and steps for running subjects.

• Installation
  • Installation on a General HPC/non-HPC System
  • Installing on Compute Canada
  • Installing on SGE (legacy)
• Basic Usage
  • Running Subjects on a General HPC/non-HPC system
  • Running Subjects on Compute Canada
  • Running Subjects on SGE (legacy)
• Customizing the pipeline to your dataset
  • Modifying init_vars
  • Supported Features
  • Modifying bb_file_manager.py to capture input files
  • Modifying IDP Generation
  • Modifying QC Generation
• Outputs
• Miscellaneous Tools
• Examples