Ruffus
Ruffus provides a Python library for building computation pipelines used in science and bioinformatics.
About Ruffus
Ruffus is a Python library for building computation pipelines, aimed at automating scientific and bioinformatics analyses with minimal setup. It is designed to stay lightweight for simple tasks while handling complex pipelines, and it uses standard Python without pre-processing or a separate configuration language.
Key features
- Builds computation pipelines in standard Python without pre-processing
- Handles simple tasks and complex, recursive-style pipelines
- Installable from PyPI with pip install ruffus --upgrade
- Latest development code obtainable via git clone
- Documentation includes tutorial, PDF manual, FAQ and cheat sheet
- Mailing list plus bug and feature request posting
Best for: Scientists and bioinformaticians who write Python and want to automate analysis pipelines.
Good for
- Lightweight syntax intended for the simplest tasks
- Scales to complicated pipelines without custom pre-processing
- Available as an easy-installable package on the Python Package Index
Watch out for
- It is a library installed and driven locally in Python, not a hosted service
Ruffus at a glance
- Website
- ruffus.org.uk
- Category
- Development › Developer Tools
- Type
- Website
- Pricing
- Not confirmed. Check the site
- Platforms
- Web
- Open source
- Not stated
- Language
- English
- Last checked
- Oct 6, 2026 · Online when checked
- Listed
- Oct 5, 2026
Guides for Developer Tools
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Ruffus FAQ
How do I install Ruffus?
It is available as an easy-installable package on the Python Package Index; run sudo pip install ruffus --upgrade or easy_install -U ruffus.
How should Ruffus be cited?
Cite Leo Goodstadt (2010), Ruffus: a lightweight Python library for computational pipelines, Bioinformatics 26(21): 2778-2779.
Where can I get the latest development code?
The in-development code can be obtained with git clone from the project's Google Code repository.
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