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bistro is an OCaml library to describe and run scientific workflows. It is dependency-aware and features distributed execution, resume-on-failure, static verification of file formats and logging facilities. Complex workflows up to tens of thousands of steps can be expressed in a concise and declarative manner, while many technical details are taken in charge by the library at no cost for the user: dependency tracking between steps, checks on file formats and argument types, installation of required computational tools, caching of previous results.

Getting started

Want to have a try? This is how to install bistro on your system

A primer on OCaml

Very little knowledge of OCaml is necessary to use the library, and we provide a short primer to get the basics. Of course, if you know more OCaml, you'll be able to create even more powerful applications with bistro like customizable pipelines or web/graphical interfaces to your pipelines.

Tutorial on analyzing RNA-seq data

Let's see how to use bistro to build a full pipeline for transcriptome data analysis on model species.