ruffus

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Overview

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The Ruffus module is a lightweight way to add support
for running computational pipelines.

Computational pipelines are often conceptually quite simple, especially
if we breakdown the process into simple stages, or separate **tasks**.

Each stage or **task** in a computational pipeline is represented by a python function
Each python function can be called in parallel to run multiple **jobs**.

Ruffus was originally designed for use in bioinformatics to analyse multiple genome
data sets.

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Documentation

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Ruffus documentation can be found `here <http://www.ruffus.org.uk>`__ ,
with `download notes <http://www.ruffus.org.uk/installation.html>`__ ,
a `tutorial <http://www.ruffus.org.uk/tutorials/new_tutorial/introduction.html>`__ and
an `in-depth manual <http://www.ruffus.org.uk/tutorials/new_tutorial/manual_contents.html>`__ .

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Background

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The purpose of a pipeline is to determine automatically which parts of a multi-stage
process needs to be run and in what order in order to reach an objective ("targets")

Computational pipelines, especially for analysing large scientific datasets are
in widespread use.
However, even a conceptually simple series of steps can be difficult to set up and
maintain.

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Design

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The ruffus module has the following design goals:

    * Lightweight
    * Scalable / Flexible / Powerful
    * Standard Python
    * Unintrusive
    * As simple as possible

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Features

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Automatic support for

    * Managing dependencies
    * Parallel jobs, including dispatching work to computational clusters
    * Re-starting from arbitrary points, especially after errors (checkpointing)
    * Display of the pipeline as a flowchart
    * Managing complex pipeline topologies

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A Simple example

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    Use the **@follows(...)** python decorator before the function definitions::

        from ruffus import *
        import sys

        def first_task():
            print "First task"

        @follows(first_task)
        def second_task():
            print "Second task"

        @follows(second_task)
        def final_task():
            print "Final task"




    the ``@follows`` decorator indicate that the ``first_task`` function precedes ``second_task`` in
    the pipeline.

    The canonical Ruffus decorator is ``@transform`` which **transforms** data flowing down a
    computational pipeline from one stage to teh next.

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Usage

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Each stage or **task** in a computational pipeline is represented by a python function
Each python function can be called in parallel to run multiple **jobs**.

1. Import module::

        import ruffus


1. Annotate functions with python decorators

2. Print dependency graph if you necessary

    - For a graphical flowchart in ``jpg``, ``svg``, ``dot``, ``png``, ``ps``, ``gif`` formats::

        pipeline_printout_graph ("flowchart.svg")

    This requires ``dot`` to be installed

    - For a text printout of all jobs ::

        pipeline_printout(sys.stdout)


3. Run the pipeline::

    pipeline_run()