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All Projects → pveber → bistro

pveber / bistro

Licence: other
A library to build and execute typed scientific workflows

Programming Languages

ocaml
1615 projects

Labels

workflowbioinformaticspipelinecomputational-biology

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bistro: build and run distributed workflows

bistro is an OCaml library to build and run computations represented by a collection of interdependent scripts, as is often found in applied research (especially computational biology).

Features:

  • build complex and composable workflows declaratively
  • simple and lightweight wrapping of new components
  • resume-on-failure: if something fails, fix it and the workflow will restart from where it stopped
  • distributed workflow execution
  • development-friendly: when a script is modified, bistro automatically finds out what needs to be recomputed
  • automatic naming of generated files
  • static typing: detect file format errors at compile time!

The library provides a datatype to represent scripts (including metadata and dependencies), an engine to run workflows and a standard library providing components for popular tools (although mostly related to computational biology and unix for now).

Questions, suggestions or contributions are welcome, please file an issue as needed.

Documentation

A manual is available, but feel free to file issues if something is unclear or missing. There is also a generated API documentation.

Installation

Detailed instructions are available in the manual. In a nutshell, bistro can be installed using opam. You need a recent (at least 4.03.0) installation of OCaml. Once this is done, simply type

opam install bistro

to install the library, or:

opam pin add -y bistro --dev-repo

to get the current development version.

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