package bistro-bio

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Bistro workflows for computational biology

Install

Dune Dependency

Authors

Maintainers

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.

Published: 15 Nov 2021

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

Used by

None

Conflicts

None

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