railroadtracks
  • Introduction
  • Installation
    • Requirements
    • Installation
  • Tutorial
    • Creating a project
    • Displaying a project
    • Working with model environments
    • Aligning reads using bowtie2
    • Task execution
    • The graph in the dependency graph
    • Building a full pipeline
      • Building blocks for the pipeline
        • 1/4: Align the reads
        • 2/4: Quantify the alignments
        • 3/4: Build a table of counts
        • 4/4: Save unaligned reads into FASTQ files
      • Assembly of the pipeline
    • Handling results (target assets)
      • Results from one task
      • Handling several alternative results
  • Cookbook
    • Environment
      • Checking that 3rd-party executables are present
    • Project
      • Get all tasks of a given type
      • Get all tasks matching a list of types
      • Get all tasks fulfilling a given activity
    • TaskSet
      • Subset all tasks with a given status
      • Subset all tasks ready for execution
      • Get all child tasks for a TaskSet
    • TaskSetGraph
      • Execute all tasks
  • Recipes
    • Steps and assets
      • Concept
      • Unspecified assets
      • Notes about the design
    • Setup
    • Simple recipe
    • Loops, nested loops, and many variants
    • Docstrings
    • Troubleshooting
  • Model
    • Overview
    • Activities
    • Inheritance diagram
    • Docstrings
  • Extending the framework
    • Writing custom steps
      • Simple case
      • Steps performing several activities
    • Unified execution
  • Unified execution
    • Version number
    • Running a step
    • Using a scheduler/Queueing system
    • Docstrings
  • Persistence
 
railroadtracks
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  • Tutorial
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TutorialΒΆ

The ipython notebook for this tutorial as standalone files [ html | pynb ]

The tutorial can otherwise be followed one section at a time:

  • Creating a project
  • Displaying a project
  • Working with model environments
  • Aligning reads using bowtie2
  • Task execution
  • The graph in the dependency graph
  • Building a full pipeline
    • Building blocks for the pipeline
    • Assembly of the pipeline
  • Handling results (target assets)
    • Results from one task
    • Handling several alternative results
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