NAME
App::Pipeline::Simple - Simple workflow manager
VERSION
version 0.9.1
SYNOPSIS
# called from a scriptDESCRIPTION
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 DEBUGconfig
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
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.