App::Pipeline::Simple - Simple workflow manager
# called from a script
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.
Constructor for the class. One instance represents the whole pipeline, and other instances are created for each step in the pipeline.
Controls logging output. Defaults to 0.
Setting verbose sets the logging level:
verbose = -1 0 1 log level => WARN INFO DEBUG
Read in the named config file.
ID of the step
Verbose description of the step
Name of the program that will be executed
Path to the directory where the program resides. Can be used if the program is not on path. Will be prepended to the name.
ID of the next step in execution. It typically depends on the output of this step.
Value read in interactively from command line
Type of input for the command line value
The ID of the step to start the execution
The ID of the step to stop the execution
Working directory where all files are stored.
Returns the step by its ID.
Return an array of steps after this one.
Return all steps.
Run this step and call the one(s).
Run in debug mode and test the configuration file
Reference to the internal Log::Logger4perl object
Transcribe the step into a UNIX command line string ready for display or execution.
Analyze the configuration without executing it.
Create a GraphViz dot file from the config.
Heikki Lehvaslaiho, KAUST (King Abdullah University of Science and Technology).
This software is copyright (c) 2012 by Heikki Lehvaslaiho.