package bistro-bio

Not available on OCaml 5.5
  1. Overview
  2. Docs
Bistro workflows for computational biology

Install 

dune-project
 Dependency

github.com Readme Edit opam file Versions (1)

Authors

  1. P
    Philippe Veber

Maintainers

  1. P
    philippe.veber@gmail.com

Sources

bistro-0.6.0.tbz
sha256=146177faaaa9117a8e2bf0fd60cb658662c0aa992f35beb246e6fd0766050e66
sha512=553fe0c20f236316449b077a47e6e12626d193ba1916e9da233e5526dd39090e8677277e1c79baace3bdc940cb009f25431730a8efc00ae4ed9cc42a0add9609

Description

This library provides wrappers for popular tools for genomics, transcriptomics and phylogeny, as well as custom tools to help piping data from one tool to the other.

Added to opam-repository:

README

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.

Dev Dependencies

None

Optional Dependencies

None

Used by

None

Conflicts

None

Build status

Results of building bistro-bio with each compiler on check.ci.ocaml.org, run of against opam-repository 8a77e58. All results for this package.

Each result links to its build log. To keep crawlers from overloading the site, build logs require a GitHub sign-in (see ocurrent/opam-health-check). On your first log, GitHub asks you to “Authorize opam-health-check”, the OCurrent app that runs these checks; it sees only your public profile, not your repositories. The sign-in lasts 30 days.

Version OCaml 4.11 OCaml 4.14 OCaml 5.2 OCaml 5.4 OCaml 5.5
0.6.0 (this version) good good n/a n/a n/a
  • good Package successfully built
  • partial One of the dependencies failed to build
  • bad Package failed to build
  • n/a Package is not available in this environment
  • internal Internal failure