Overview
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.
Documentation
Ruffus documentation can be found here , with download notes , a tutorial and an in-depth manual .
Background
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.
Design
The ruffus module has the following design goals:
Lightweight
Scalable / Flexible / Powerful
Standard Python
Unintrusive
As simple as possible
Features
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
A Simple example
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.
Usage
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.
Import module:
import ruffus
Annotate functions with python decorators
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)Run the pipeline:
pipeline_run()
Release files for ruffus 3.0.0
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| ruffus-3.0.0.tar.gz | 12.2 MB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| ruffus-3.0.0-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 12.4 MB
Release files / ruffus-3.0.0.tar.gz
| Download URL | ruffus-3.0.0.tar.gz |
|---|---|
| Size | 12.2 MB |
| Tags | Source |
|
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Release files / ruffus-3.0.0-py3-none-any.whl
| Download URL | ruffus-3.0.0-py3-none-any.whl |
|---|---|
| Size | 249.9 kB |
| Tags | Python 3 |
|
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