Package fr.ens.biologie.genomique.eoulsan.modules.diffana

Class RModuleCommonConfiguration

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration

public class RModuleCommonConfiguration
extends Object

This class define common methods used for the configuration of the step of the package.

Since:

2.0

Author:

Laurent Jourdren

Field Summary

Fields

Modifier and Type	Field	Description
static final String	DOCKER_IMAGE_PARAMETER
static final String	EXECUTION_MODE_PARAMETER
static final String	RSERVE_SERVER_PARAMETER

Constructor Summary

Constructors

Constructor	Description
RModuleCommonConfiguration()

Method Summary

Modifier and Type	Method	Description
static RExecutor	parseRExecutorParameter(StepConfigurationContext context, Set<Parameter> stepParameters, Set<Requirement> requirements, String defaultDockerImage)	Parse the step parameter and create a configured RExecutor object.

Methods inherited from class java.lang.Object

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

Field Details

EXECUTION_MODE_PARAMETER

public static final String EXECUTION_MODE_PARAMETER

See Also:

• Constant Field Values

RSERVE_SERVER_PARAMETER

public static final String RSERVE_SERVER_PARAMETER

See Also:

• Constant Field Values

DOCKER_IMAGE_PARAMETER

public static final String DOCKER_IMAGE_PARAMETER

See Also:

• Constant Field Values

Constructor Details

RModuleCommonConfiguration

public RModuleCommonConfiguration()

Method Details

parseRExecutorParameter

public static RExecutor parseRExecutorParameter(StepConfigurationContext context,
 Set<Parameter> stepParameters,
 Set<Requirement> requirements,
 String defaultDockerImage)
                                         throws EoulsanException

Parse the step parameter and create a configured RExecutor object.

Parameters:

context - the step context

stepParameters - the step parameters. Must be a mutable object

requirements - the requirements

defaultDockerImage - default docker image

Returns:

a configured RExecutor object

Throws:

EoulsanException - if one or more parameter is invalid