package bistro

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Base types
Building shell-based workflow
File formats

bistro
- Bistro
  - Private
  - Shell_dsl
  - Template_dsl
  - Workflow
  - binary_file
  - bz2
  - csv
  - directory_t
  - gz
  - html
  - pdf
  - png
  - regular_file_t
  - sexp_value
  - svg
  - tar
  - text
  - tsv
  - zip
bistro.engine
- Bistro_engine
  - Allocator
  - Db
  - Docker
  - Eval_thread
    
    Infix
  - Execution_env
  - Execution_trace
    
    Outcome
    
    Run_details
    
    Set
  - Local_backend
  - Logger
    
    t
  - Lwt_queue
  - Misc
  - Path
  - Scheduler
    
    Backend
    
    Gc
    
    Make
    
    Backend
  - Shell_command
  - Singularity
bistro.internals
- Bistro_internals
  - Command
  - Template
  - Workflow
    
    Any
    
    Map
    
    Set
    
    T
    
    Table
    
    Docker_image
    
    Singularity_image
bistro.multinode
- Bistro_multinode
  - Client
  - Server
bistro.nlp
- Bistro_nlp
  - Stanford_parser
    
    deps
bistro.script
- Bistro_script
bistro.unix
- Bistro_unix
  - Cmd
bistro.utils
- Bistro_utils
  - Console_logger
  - Dot_output
  - Html_logger
  - R_script
  - Repo
  - Report
    
    Md
  - Toplevel_eval
    
    Make
    
    P

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Module
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Class type

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

type '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.

type '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).

class type regular_file_t = object ... end

Base class for files when typing a path

class type directory_t = object ... end

Base class for directories when typing a path

type 'a file = regular_file_t as 'a path workflow

Type alias for workflows that produce a regular file

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

Type alias for workflows that produce a directory

Building shell-based workflow

type container_image

module Template_dsl : sig ... end

Representation of scripts

module Shell_dsl : sig ... end

Command-line construction

module Workflow : sig ... end

Workflow constructors

File formats

class type text = object ... end

class type 'a sexp_value = object ... end

class type binary_file = object ... end

class type pdf = object ... end

class type html = object ... end

class type png = object ... end

class type svg = object ... end

class type tsv = object ... end

class type csv = object ... end

class type 'a zip = object ... end

class type 'a gz = object ... end

class type 'a bz2 = object ... end

class type 'a tar = object ... end

module Private : sig ... end

Access to internal representation