https://github.com/pveber/bistro

A library to build and execute typed scientific workflows
https://github.com/pveber/bistro

bioinformatics computational-biology ocaml pipeline workflow

Last synced: about 1 month ago
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A library to build and execute typed scientific workflows

• Host: GitHub
• URL: https://github.com/pveber/bistro
• Owner: pveber
• License: other
• Created: 2014-01-19T15:30:29.000Z (almost 11 years ago)
• Default Branch: master
• Last Pushed: 2024-05-17T19:53:47.000Z (6 months ago)
• Last Synced: 2024-09-30T06:41:16.248Z (about 2 months ago)
• Topics: bioinformatics, computational-biology, ocaml, pipeline, workflow
• Language: OCaml
• Homepage:
• Size: 1.56 MB
• Stars: 46
• Watchers: 8
• Forks: 10
• Open Issues: 15
• Metadata Files:
  • Readme: README.md
  • Changelog: Changes
  • License: LICENSE

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README

        
# bistro: build and run distributed workflows

`bistro` is an [OCaml](http://ocaml.org) 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](https://github.com/pveber/bistro/issues) as needed.

## Documentation

A

[manual](http://bistro.readthedocs.io/en/latest/getting-started.html)

is available, but feel free to file issues if something is unclear or

missing. There is also a

[generated API documentation](http://pveber.github.io/bistro/).

## Installation

Detailed instructions are available in the

[manual](http://bistro.readthedocs.io/en/latest/getting-started.html). In

a nutshell, `bistro` can be installed using

[opam](http://opam.ocaml.org/). 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.