package bistro

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A library to build and run distributed scientific workflows

Install

Dune Dependency

github.com Readme Edit opam file Versions (2)

Authors

P

Philippe Veber

Maintainers

P

philippe.veber@gmail.com

Sources

bistro-0.6.0.tbz

sha256=146177faaaa9117a8e2bf0fd60cb658662c0aa992f35beb246e6fd0766050e66

sha512=553fe0c20f236316449b077a47e6e12626d193ba1916e9da233e5526dd39090e8677277e1c79baace3bdc940cb009f25431730a8efc00ae4ed9cc42a0add9609

doc/bistro/Bistro/index.html

Module `Bistro`Source

A library to build scientific workflows.

This module introduces a type 'a workflow that describes a set of inter-dependent steps that will eventually generate a value of type 'a. Steps may be either command lines to be executed, or OCaml expressions to be evaluated.

To build shell-based workflows, use the Shell_dsl module, that provides a set of combinators to write shell scripts easily. For instance, the following function shows how to create a gzipped file using the output of another workflow:

  let gzip (x : 'a pworkflow) : 'a gz pworkflow =
    Workflow.shell ~descr:"unix.gzip" [
      cmd "gzip" [ string "-c" ; dep x ; string ">" dest ]
    ]

Base types

Sourcetype 'a workflow

Representation of a computational pipeline. Constructors are provided in the Workflow module. Note that a workflow is just a recipe to build some result. Building the workflow won't actually generate anything. In order to run the workflow, you have to run it using an execution engine like the one provided by bistro.engine.

Sourcetype 'a path

Abstract representation of a path in the filesystem. The type parameter can be used to provide information on the format of a file (this is an instance of phantom-typing).

Sourceclass type regular_file_t = object ... end

Base class for files when typing a path

Sourceclass type directory_t = object ... end

Base class for directories when typing a path

Sourcetype 'a file = (regular_file_t as 'a) path workflow

Type alias for workflows that produce a regular file

Sourcetype 'a directory = < directory_t ; contents : 'a > path workflow

Type alias for workflows that produce a directory

Building shell-based workflow

Sourcetype container_image

Sourcemodule Template_dsl : sig ... end

Representation of scripts

Sourcemodule Shell_dsl : sig ... end

Command-line construction

Sourcemodule Workflow : sig ... end

Workflow constructors

File formats

Sourceclass type text = object ... end

Sourceclass type 'a sexp_value = object ... end

Sourceclass type binary_file = object ... end

Sourceclass type pdf = object ... end

Sourceclass type html = object ... end

Sourceclass type png = object ... end

Sourceclass type svg = object ... end

Sourceclass type tsv = object ... end

Sourceclass type csv = object ... end

Sourceclass type 'a zip = object ... end

Sourceclass type 'a gz = object ... end

Sourceclass type 'a bz2 = object ... end

Sourceclass type 'a tar = object ... end

Sourcemodule Private : sig ... end

Access to internal representation

On This Page

Base types
Building shell-based workflow
File formats