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Module Version: 0.9.1   Source  

NAME ^

App::Pipeline::Simple - Simple workflow manager

VERSION ^

version 0.9.1

SYNOPSIS ^

  # called from a script

DESCRIPTION ^

Unless you want to change or extend the module, you probably do not need to read this documentation. Runtime information is in spipe application.

Workflow management in computational (biological) sciences is a hard problem. This module is based on assumption that UNIX pipe and redirect system is closest to optimal solution with these improvements:

* Enforce the storing of all intermediate steps in a file.

  This is for clarity, accountability and to enable arbitrarily big
  data sets. Pipeline can contain independent steps that remove
  intermediate files if so required.

* Naming of each step.

  This is to make it possible to stop, restart, and restart at any
  intermediate step after adjusting pipeline parameters.

* detailed logging

  To keep track of all runs of the pipeline.

A pipeline is a collection of steps that are functionally equivalent to a pipeline. In other words, execution of a pipeline equals to execution of a each ordered step within the pipeline. From that derives that the pipeline object model needs only one class that can recursively represent the whole pipeline as well as individual steps.

METHODS ^

new

Constructor for the class. One instance represents the whole pipeline, and other instances are created for each step in the pipeline.

verbose

Controls logging output. Defaults to 0.

Setting verbose sets the logging level:

  verbose   =  -1    0     1
  log level =>  WARN INFO  DEBUG

config

Read in the named config file.

id

ID of the step

description

Verbose description of the step

name

Name of the program that will be executed

path

Path to the directory where the program resides. Can be used if the program is not on path. Will be prepended to the name.

next_id

ID of the next step in execution. It typically depends on the output of this step.

input

Value read in interactively from command line

itype

Type of input for the command line value

start

The ID of the step to start the execution

stop

The ID of the step to stop the execution

dir

Working directory where all files are stored.

step

Returns the step by its ID.

each_next

Return an array of steps after this one.

each_step

Return all steps.

run

Run this step and call the one(s).

debug

Run in debug mode and test the configuration file

logger

Reference to the internal Log::Logger4perl object

render

Transcribe the step into a UNIX command line string ready for display or execution.

stringify

Analyze the configuration without executing it.

graphviz

Create a GraphViz dot file from the config.

SEE ALSO ^

spipe

AUTHOR ^

Heikki Lehvaslaiho, KAUST (King Abdullah University of Science and Technology).

COPYRIGHT AND LICENSE ^

This software is copyright (c) 2012 by Heikki Lehvaslaiho.

This is free software; you can redistribute it and/or modify it under the same terms as the Perl 5 programming language system itself.

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