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