Package fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop

Class ReadsMapperHadoopModule

java.lang.Object

fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule

fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperHadoopModule

All Implemented Interfaces:

Module

public class ReadsMapperHadoopModule
extends AbstractReadsMapperModule

This class define an mapper module in Hadoop mode.

Since:

1.0

Author:

Laurent Jourdren

Field Summary

Fields inherited from class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule

COUNTER_GROUP, GENOME_DESCRIPTION_PORT_NAME, HADOOP_THREADS_PARAMETER_NAME, HADOOP_TIMEOUT, LOCAL_THREADS_PARAMETER_NAME, MAPPER_ARGUMENTS_PARAMETER_NAME, MAPPER_DOCKER_IMAGE_PARAMETER_NAME, MAPPER_FLAVOR_PARAMETER_NAME, MAPPER_INDEX_PORT_NAME, MAPPER_NAME_PARAMETER_NAME, MAPPER_VERSION_PARAMETER_NAME, MAX_LOCAL_THREADS_PARAMETER_NAME, MODULE_NAME, READS_PORT_NAME, USE_BUNDLED_BINARIES_PARAMETER_NAME

Constructor Summary

Constructors

Constructor	Description
ReadsMapperHadoopModule()

Method Summary

Modifier and Type	Method	Description
void	configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
TaskResult	execute(TaskContext context, TaskStatus status)	Execute a task step.
InputPorts	getInputPorts()	Get the input data format.

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule

getDescription, getMapper, getMapperArguments, getMapperDockerImage, getMapperFlavor, getMapperHadoopMemoryRequired, getMapperHadoopThreads, getMapperLocalThreads, getMapperName, getMapperVersion, getName, getOutputPorts, getReducerTaskCount, getVersion, isUseBundledBinaries

Methods inherited from class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule

getChecker, getParallelizationMode, getRequiredEoulsanVersion, getRequirements

Methods inherited from class java.lang.Object

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

Constructor Detail

ReadsMapperHadoopModule

public ReadsMapperHadoopModule()

Method Detail

getInputPorts

public InputPorts getInputPorts()

Description copied from interface: Module

Get the input data format.

Specified by:

getInputPorts in interface Module

Overrides:

getInputPorts in class AbstractModule

Returns:

a set with DataFormat or null if the module does not any need input format

configure

public void configure(StepConfigurationContext context,
                      Set<Parameter> stepParameters)
               throws EoulsanException

Description copied from interface: Module

Set the parameters of the step to configure the module.

Specified by:

configure in interface Module

Overrides:

configure in class AbstractReadsMapperModule

Parameters:

context - configuration context. The context can be null for generator steps

stepParameters - parameters of the step

Throws:

EoulsanException - if a parameter is invalid

execute

public TaskResult execute(TaskContext context,
                          TaskStatus status)

Description copied from interface: Module

Execute a task step.

Parameters:

context - Execution context

status - of the task