ruffus Contents Manual

Introduction

  • Installation
  • Latest Changes
  • New Object Orientated Syntax
    • Worked Example for New Object orientated syntax for Ruffus in Version 2.6
    • Python Code for: New Object orientated syntax for Ruffus in Version 2.6
  • Future plans
  • FAQ
  • Hall of Fame
  • Who is Ruffus?
  • Manual
    • Chapter 1: An introduction to basic Ruffus syntax
    • Chapter 2: Transforming data in a pipeline with @transform
    • Chapter 3: More on @transform-ing data
    • Chapter 4: Creating files with @originate
    • Chapter 5: Understanding how your pipeline works with pipeline_printout(...)
    • Chapter 6: Running Ruffus from the command line with ruffus.cmdline
    • Chapter 7: Displaying the pipeline visually with pipeline_printout_graph(...)
    • Chapter 8: Specifying output file names with formatter() and regex()
    • Chapter 9: Preparing directories for output with @mkdir()
    • Chapter 10: Checkpointing: Interrupted Pipelines and Exceptions
    • Chapter 11: Pipeline topologies and a compendium of Ruffus decorators
    • Chapter 12: Splitting up large tasks / files with @split
    • Chapter 13: @merge multiple input into a single result
    • Chapter 14: Multiprocessing, drmaa and Computation Clusters
    • Chapter 15: Logging progress through a pipeline
    • Chapter 16: @subdivide tasks to run efficiently and regroup with @collate
    • Chapter 17: @combinations, @permutations and all versus all @product
    • Chapter 18: Turning parts of the pipeline on and off at runtime with @active_if
    • Chapter 19: Signal the completion of each stage of our pipeline with @posttask
    • Chapter 20: Manipulating task inputs via string substitution using inputs() and add_inputs()
    • Chapter 21: Esoteric: Generating parameters on the fly with @files
    • Chapter 22: Esoteric: Running jobs in parallel without files using @parallel
    • Chapter 23: Esoteric: Writing custom functions to decide which jobs are up to date with @check_if_uptodate
    • Appendix 1: Flow Chart Colours with pipeline_printout_graph(...)
    • Appendix 2: How dependency is checked
    • Appendix 3: Exceptions thrown inside pipelines
    • Appendix 4: Names exported from Ruffus
    • Appendix 5: @files: Deprecated syntax
    • Appendix 6: @files_re: Deprecated syntax using regular expressions
    • Chapter 1: Python Code for An introduction to basic Ruffus syntax
    • Chapter 1: Python Code for Transforming data in a pipeline with @transform
    • Chapter 3: Python Code for More on @transform-ing data
    • Chapter 4: Python Code for Creating files with @originate
    • Chapter 5: Python Code for Understanding how your pipeline works with pipeline_printout(...)
    • Chapter 7: Python Code for Displaying the pipeline visually with pipeline_printout_graph(...)
    • Chapter 8: Python Code for Specifying output file names with formatter() and regex()
    • Chapter 9: Python Code for Preparing directories for output with @mkdir()
    • Chapter 10: Python Code for Checkpointing: Interrupted Pipelines and Exceptions
    • Chapter 12: Python Code for Splitting up large tasks / files with @split
    • Chapter 13: Python Code for @merge multiple input into a single result
    • Chapter 14: Python Code for Multiprocessing, drmaa and Computation Clusters
    • Chapter 15: Python Code for Logging progress through a pipeline
    • Chapter 16: Python Code for @subdivide tasks to run efficiently and regroup with @collate
    • Chapter 17: Python Code for @combinations, @permutations and all versus all @product
    • Chapter 20: Python Code for Manipulating task inputs via string substitution using inputs() and add_inputs()
    • Chapter 21: Esoteric: Python Code for Generating parameters on the fly with @files
    • Appendix 1: Python code for Flow Chart Colours with pipeline_printout_graph(...)
    • Construction of a simple pipeline to run BLAST jobs
    • Part 2: A slightly more practical pipeline to run blasts jobs
    • Ruffus code
    • Ruffus code
    • Example code for FAQ Good practices: "What is the best way of handling data in file pairs (or triplets etc.)?"

Reference

  • Ruffus Functions
    • pipeline_run
    • pipeline_printout
    • pipeline_printout_graph
    • pipeline_get_task_names
    • run_job
  • Ruffus Decorators
    • originate
    • split
    • transform
    • merge
    • subdivide
    • transform
    • collate
    • graphviz
    • mkdir
    • jobs_limit
    • posttask
    • active_if
    • follows
    • product
    • permutations
    • combinations
    • combinations_with_replacement
    • Parameters on the fly with @files
    • check_if_uptodate
    • parallel
    • files
    • @files_re
    • Core
    • Combinatorics
    • Advanced
    • Esoteric!
  • Indicator Objects
    • formatter
    • suffix
    • regex
    • add_inputs
    • inputs
    • mkdir
    • touch_file
    • output_from
    • combine
  • Design & Architecture
    • GNU Make
    • Scons, Rake and other Make alternatives
    • Managing pipelines stage-by-stage using Ruffus
    • Alternatives to Ruffus
  • Implementation Tips
    • Release
    • blogger
    • dbdict.py
    • how to write new decorators
  • Implementation notes
    • Ctrl-C handling
    • Python3 compatability
    • Refactoring: parameter handling
    • formatter
    • @product()
    • @permutations(...), @combinations(...), @combinations_with_replacement(...)
    • drmaa alternatives
    • Task completion monitoring
    • @mkdir(...),
    • Parameter handling
    • Add Object Orientated interface
  • Cheat Sheet
    • 1. Annotate functions with Ruffus decorators
    • 2. Print dependency graph if necessary
    • 3. Run the pipeline
  • Glossary
  • ruffus.Task
    • Decorators
    • Pipeline functions
    • Logging
    • Implementation:
    • Exceptions and Errors
  • ruffus.proxy_logger
    • Create proxy for logging for use with multiprocessing
    • Proxies for a log:
    • Create a logging object
 
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Ruffus documentation¶

Start Here:¶

Introduction¶

  • Installation
  • Latest Changes
  • New Object Orientated Syntax
  • Future plans
  • FAQ
  • Hall of Fame
  • Who is Ruffus?
  • Manual

Quick Reference:¶

Reference¶

  • Ruffus Functions
  • Ruffus Decorators
  • Indicator Objects

Indices and tables¶

  • Index
  • Module Index
  • Search Page
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