biolockj

Class Summary
Class	Description
BioLockJ	This is the primary BioLockJ class - its main() method is executed when the jar is run. This class validates the runtime parameters to run a new pipeline or restart a failed pipeline. The Java log file is initialized and the configuration file is processed before starting the pipeline. If the pipeline is successful, the program executes clean up operations (if configured) and creates a status-complete indicator file in the pipeline root directory.
BioModuleFactory	This class initializes pipeline modules, starting with those in the Config file and adding the prerequisite and post-requisite modules.
Config	Provides type-safe, validated methods for storing/accessing system properties. Initially populated by the properties in the Config file, several additional properties are created and stored in the the Config (to save system determined info such as: pipeline directory and name, has paired reads?, has multiplexed reads?, etc.).
Constants	Single Java class to hold shared constant values referenced my multiple classes.
Log	Simple Logging Facade for Java (SLF4J) implementation using Log4J Log4J Configuration: log4j.properties Every Java class that prints to the Java log file, will do so by calling: `Log.out(Class)`.`Log.out(Class)`.debug( logMessage ) `Log.out(Class)`.`Log.out(Class)`.info( logMessage ) `Log.out(Class)`.`Log.out(Class)`.warn( logMessage ) `Log.out(Class)`.`Log.out(Class)`.error( logMessage, exception )
Pipeline	This class initializes and executes each `BioModule` configured for execution. `BioModule`s that generate scripts are monitored until all scripts are complete, before moving on to the next module.
Processor	`ScriptModule`s that generate scripts will submit a main script to the OS for execution as a `Processor`.
Properties	Load properties defined in the BioLockJ configuration file, including inherited properties from project.defaultProps

Package biolockj Description

The root biolockj package contains core classes used by all BioLockJ pipelines.

To start a new pipeline:

java biolockj.BiolockJ $CONFIG_PATH

To restart a failed pipeline add the "r" parameter.

java biolockj.BiolockJ $CONFIG_PATH r

java biolockj.BiolockJ $CONFIG_PATH restart