bistro

A library to build and run distributed scientific workflows
README

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.

Install
Published
21 Aug 2019
Sources
v0.5.0.tar.gz
md5=0ccb7c97728c94d17494b150192f6162
sha512=61dbd0ee5b98cd5fb8871d653aef0e440c318e9fbca439c3b0e4f86a32fa03c2a8a4770cd96b929b21b378db6788fa7d4df15935370be5b7b227564a31994998
Dependencies
re
>= "1.7.2"
tyxml
>= "4.3"
sexplib
>= "113.24.00" & < "v0.13"
ppx_sexp_conv
< "v0.13"
ppxlib
< "0.23.0"
ocamlgraph
>= "1.8.7"
lwt
>= "3.2.0"
core
>= "v0.12.0" & < "v0.13"
dune
>= "1.11"
base64
>= "3.0.0"
ocaml
>= "4.07.0"
Reverse Dependencies