NAME App::Pipeline::Simple - Simple workflow manager VERSION version 0.9.0 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 object 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. 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.