CGAT Pipelines

• Installing CGAT pipelines
  • Downloading and installing the source code
  • Setting up the computing environment
  • Software requirements
• Using CGAT pipelines
  • Introduction
  • Setting up a pipeline
  • Running a pipeline
  • Building pipeline reports
• Building CGAT pipelines
  • Overview
  • Guidelines
  • Running commands within tasks
  • Tracks
  • Databases
  • Reports
  • Configuration values
  • Documentation
  • Using other pipelines
  • Publishing data
  • Checking requisites
• Writing pipeline reports
  • Background
  • Advanced topics
• Background
• NGS Pipelines
  • Genomics Pipelines
  • NGS Pipelines
  • Other pipelines
  • Obsolete pipelines
• Lecgacy pipelines
  • Transcript comparison pipeline
  • GPipe - Gene prediction pipeline
  • 454 Transcript mapping pipeline
  • OPTIC