Package fr.ens.biologie.genomique.eoulsan.core.workflow

Class CommandStep

java.lang.Object

fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep

fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep

All Implemented Interfaces:

Step, Serializable

public class CommandStep
extends AbstractStep

This class define a step based on a Command object (workflow file).

Since:

2.0

Author:

Laurent Jourdren

See Also:

Serialized Form

Nested Class Summary

Nested classes/interfaces inherited from interface fr.ens.biologie.genomique.eoulsan.core.Step

Step.DiscardOutput, Step.StepState, Step.StepType

Constructor Summary

Constructors

Constructor	Description
CommandStep(AbstractWorkflow workflow, Module module)	Create a step for a standard step from an existing step object.
CommandStep(AbstractWorkflow workflow, Module module, Set<Parameter> parameters)	Create a step for a standard step from an existing step object.
CommandStep(AbstractWorkflow workflow, Step.StepType type)	Constructor that create a step with nothing to execute like ROOT_STEP, DESIGN_STEP and FIRST_STEP.
CommandStep(AbstractWorkflow workflow, DataFormat format)	Create a Generator Workflow step.
CommandStep(AbstractWorkflow workflow, String id, String moduleName, String stepVersion, Set<Parameter> parameters, boolean skip, Step.DiscardOutput discardOutput, int requiredMemory, int requiredProcessors, String dataProduct)	Create a step for a standard step.
CommandStep(AbstractWorkflow workflow, String id, String moduleName, String stepVersion, Set<Parameter> parameters, boolean skip, Step.DiscardOutput discardOutput, int requiredMemory, int requiredProcessors, String dataProduct, DataFile outputDirectory)	Create a step for a standard step.

Method Summary

Methods inherited from class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep

addDependency, addDependency, configure, getChecker, getDiscardOutput, getEoulsanMode, getId, getInputPorts, getModule, getModuleName, getNumber, getOutputPorts, getParallelizationMode, getParameters, getRequiredMemory, getRequiredProcessors, getState, getStepOutputDirectory, getStepVersion, getType, getWorkflow, isSkip, isTerminalStep, registerInputAndOutputPorts

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CommandStep

public CommandStep(AbstractWorkflow workflow,
                   Step.StepType type)

Constructor that create a step with nothing to execute like ROOT_STEP, DESIGN_STEP and FIRST_STEP.

Parameters:

workflow - the workflow of the step

type - the type of the step

CommandStep

public CommandStep(AbstractWorkflow workflow,
                   DataFormat format)
            throws EoulsanException

Create a Generator Workflow step.

Parameters:

workflow - the workflow object

format - DataFormat

Throws:

EoulsanException - if an error occurs while configuring the generator

CommandStep

public CommandStep(AbstractWorkflow workflow,
                   String id,
                   String moduleName,
                   String stepVersion,
                   Set<Parameter> parameters,
                   boolean skip,
                   Step.DiscardOutput discardOutput,
                   int requiredMemory,
                   int requiredProcessors,
                   String dataProduct)
            throws EoulsanException

Create a step for a standard step.

Parameters:

workflow - workflow of the step

id - identifier of the step

moduleName - module name

stepVersion - step version

parameters - parameters of the step

skip - true to skip execution of the step

discardOutput - discard output value

requiredMemory - required memory

requiredProcessors - required processors

dataProduct - data product

Throws:

EoulsanException - id an error occurs while creating the step

CommandStep

public CommandStep(AbstractWorkflow workflow,
                   String id,
                   String moduleName,
                   String stepVersion,
                   Set<Parameter> parameters,
                   boolean skip,
                   Step.DiscardOutput discardOutput,
                   int requiredMemory,
                   int requiredProcessors,
                   String dataProduct,
                   DataFile outputDirectory)
            throws EoulsanException

Create a step for a standard step.

Parameters:

workflow - workflow of the step

id - identifier of the step

moduleName - module name

stepVersion - step version

parameters - parameters of the step

skip - true to skip execution of the step

discardOutput - discard output value

requiredMemory - required memory

requiredProcessors - required processors

dataProduct - data product

outputDirectory - output directory

Throws:

EoulsanException - id an error occurs while creating the step

CommandStep

public CommandStep(AbstractWorkflow workflow,
                   Module module)
            throws EoulsanException

Create a step for a standard step from an existing step object.

Parameters:

workflow - workflow of the step

module - module object

Throws:

EoulsanException - id an error occurs while creating the step

CommandStep

public CommandStep(AbstractWorkflow workflow,
                   Module module,
                   Set<Parameter> parameters)
            throws EoulsanException

Create a step for a standard step from an existing step object.

Parameters:

workflow - workflow of the step

module - module object

parameters - parameters of the step

Throws:

EoulsanException - id an error occurs while creating the step