Uses of Class
fr.ens.biologie.genomique.eoulsan.EoulsanException

Packages that use EoulsanException

Package	Description
fr.ens.biologie.genomique.eoulsan	Root package of Eoulsan.
fr.ens.biologie.genomique.eoulsan.checkers	This package contains and define checkers of DataFormat.
fr.ens.biologie.genomique.eoulsan.core	This package contains Eoulsan workflow core class.
fr.ens.biologie.genomique.eoulsan.core.schedulers	This package contains classes for schedulers.
fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters	This package contains classes for cluster schedulers.
fr.ens.biologie.genomique.eoulsan.core.workflow	This package contains Eoulsan workflow dedicated classes.
fr.ens.biologie.genomique.eoulsan.data	This package contains classes for data files, data types and data formats.
fr.ens.biologie.genomique.eoulsan.design	This package contains classes to handle experimental designs.
fr.ens.biologie.genomique.eoulsan.galaxytools	This package contain classes related to read tool xml file from galaxy.
fr.ens.biologie.genomique.eoulsan.galaxytools.elements	This package contain classes related to parameter extractions from XML Galaxy tool xml files.
fr.ens.biologie.genomique.eoulsan.modules	This package define the steps for the Eoulsan workflow.
fr.ens.biologie.genomique.eoulsan.modules.chipseq	This packages contains the ChIP-Seq modules.
fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling	This packages contains the peak-calling modules.
fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc	This packages contains all the quality check modules for ChIP-Seq.
fr.ens.biologie.genomique.eoulsan.modules.diffana	This package contain all the classes related to the differential analysis step.
fr.ens.biologie.genomique.eoulsan.modules.expression	This package contain all the classes related to the expression step.
fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop	This package contain all the classes related to the expression step in hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.fastqc	This package contain all the classes related to FastQC.
fr.ens.biologie.genomique.eoulsan.modules.generators	This package contain generator steps.
fr.ens.biologie.genomique.eoulsan.modules.mapping	This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step.
fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop	This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop	This package contain classes related data management in Hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload	This package contain classes related to upload data to HDFS and Cloud.
fr.ens.biologie.genomique.eoulsan.modules.multiqc
fr.ens.biologie.genomique.eoulsan.modules.singlecell
fr.ens.biologie.genomique.eoulsan.requirements	This package contains requirement classes for Eoulsan.
fr.ens.biologie.genomique.eoulsan.splitermergers	This package contains splitter and merger used when running Eoulsan on a standard cluster to get more parallelization efficiency.
fr.ens.biologie.genomique.eoulsan.util	This package contain utility classes.
fr.ens.biologie.genomique.eoulsan.util.hadoop	This package contains utility classes for hadoopS.
fr.ens.biologie.genomique.eoulsan.util.locker	This package contain an advanced multi JVM lock system.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan

Methods in fr.ens.biologie.genomique.eoulsan that throw EoulsanException

Modifier and Type	Method	Description
void	Main.createLogFileAndFlushLog(URI logFilename)	Create a new log file and flush log.
void	Main.createLogFiles(URI EoulsanlogFilename, URI otherlogFilename)	Create the log file for Eoulsan and additional log file for dependencies that use their own logging system.
double	Settings.getDoubleSetting(String settingName)	Get the value of the setting as a double value
int	Settings.getIntSetting(String settingName)	Get the value of the setting as a integer value
static void	LocalEoulsanRuntime.initEoulsanRuntimeForExternalApp()	Initialization Eoulsan runtime for external application who needed Eoulsan
protected abstract void	Main.initializeRuntime(Settings settings)	Initialize the Eoulsan runtime.
void	Settings.loadSettings()	Load application options.
void	Settings.loadSettings(File file)	Load application options.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.checkers

Methods in fr.ens.biologie.genomique.eoulsan.checkers that throw EoulsanException

Modifier and Type	Method	Description
boolean	Checker.check(Data data, CheckStore checkInfo)	Launch the check.
boolean	DESeq2DesignChecker.check(Data data, CheckStore checkInfo)
boolean	GenomeChecker.check(Data data, CheckStore checkInfo)
boolean	GFFChecker.check(Data data, CheckStore checkInfo)
boolean	ReadsChecker.check(Data data, CheckStore checkInfo)
static boolean	DESeq2DesignChecker.checkExperimentDesign(Experiment experiment)	Check experiment design.
void	Checker.configure(Set<Parameter> stepParameters)	Set the parameters of the checker to configure the checker.
void	DESeq2DesignChecker.configure(Set<Parameter> stepParameters)
void	GenomeChecker.configure(Set<Parameter> stepParameters)
void	GFFChecker.configure(Set<Parameter> stepParameters)
void	ReadsChecker.configure(Set<Parameter> stepParameters)

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.core

Methods in fr.ens.biologie.genomique.eoulsan.core that throw EoulsanException

Modifier and Type	Method	Description
static void	Modules.badParameterValue(StepConfigurationContext context, Parameter parameter, String message)	Throw a exception for bad parameter value.
static void	Modules.badParameterValue(String stepId, Parameter parameter, String message)	Throw a exception for bad parameter value.
void	Module.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the module.
static void	Modules.deprecatedParameter(StepConfigurationContext context, Parameter parameter, boolean throwException)	Show a message for deprecated parameters.
static void	Modules.deprecatedParameter(String stepId, Parameter parameter, boolean throwException)	Show a message for deprecated parameters.
double	Parameter.getDoubleValue()	Get the value of the parameter as a double value.
int	Parameter.getIntValue()	Get the value of the parameter as a integer value.
int	Parameter.getIntValueGreaterOrEqualsTo(int min)	* Get the value of the parameter as a integer value and check if this value is greater or equals to the min parameter value.
int	Parameter.getIntValueInRange(int min, int max)	Get the value of the parameter as a integer value and check if this value is in the correct range.
static void	Modules.invalidConfiguration(StepConfigurationContext context, String message)	Throw a exception for an invalid configuration.
static void	Modules.invalidConfiguration(String stepId, String message)	Throw a exception for an invalid configuration.
static Step.DiscardOutput	Step.DiscardOutput.parse(String s)	This method define a parser for the values of the "discardoutput" attribute of the Eoulsan workflow.
static void	Modules.removedParameter(StepConfigurationContext context, Parameter parameter)	Throw a exception for removed parameters.
static void	Modules.removedParameter(String stepId, Parameter parameter)	Throw a exception for removed parameters.
static void	Modules.renamedParameter(StepConfigurationContext context, Parameter parameter, String newParameterName, boolean throwException)	Show a message for deprecated parameters that has been renamed.
static void	Modules.renamedParameter(String stepId, Parameter parameter, String newParameterName, boolean throwException)	Show a message for deprecated parameters that has been renamed.
static void	Modules.unknownParameter(StepConfigurationContext context, Parameter parameter)	Throw a exception for unknown parameters.
static void	Modules.unknownParameter(String stepId, Parameter parameter)	Throw a exception for unknown parameters.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.core.schedulers

Methods in fr.ens.biologie.genomique.eoulsan.core.schedulers that throw EoulsanException

Modifier and Type	Method	Description
static void	TaskSchedulerFactory.initialize()

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters

Methods in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters that throw EoulsanException

Modifier and Type	Method	Description
void	BpipeTaskScheduler.configure(Settings settings)
void	ClusterTaskScheduler.configure(Settings settings)	Configure the scheduler.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.core.workflow

Methods in fr.ens.biologie.genomique.eoulsan.core.workflow that throw EoulsanException

Modifier and Type	Method	Description
void	CommandWorkflowParser.addConstant(String constantName, String constantValue)	Add a constant.
void	CommandWorkflowParser.addConstant(String constantName, String constantValue, boolean evaluateValue)	Add a constant.
void	CommandWorkflowParser.addConstants(ExecutorArguments arguments)	Add job arguments information to constants.
void	AbstractWorkflow.checkDirectories()	Check directories needed by the workflow.
protected void	AbstractStep.configure()	Configure the step.
void	AbstractWorkflow.createEoulsanDataDirectoryIfRequired()	Create an "eoulsan-data" directory if mapper indexes or genome description storage has not been defined.
void	AbstractWorkflow.execute()	Execute the workflow.
void	Executor.execute()	run Eoulsan.
void	Executor.execute(List<Module> firstSteps, List<Module> lastSteps)	run Eoulsan.
static TaskResultImpl	TaskSerializationUtils.execute(DataFile taskContextFile)	Execute a task context serialization file.
static TaskResultImpl	TaskSerializationUtils.execute(DataFile taskContextFile, DataFile outputDir)	Execute a task context serialization file.
Module	StepInstances.getModule(Step step, String moduleName, String moduleVersion)	Get a step instance.
CommandWorkflowModel	CommandWorkflowParser.parse()	Parse the workflow file.
protected void	AbstractWorkflow.saveConfigurationFiles()	Save configuration files.
protected void	CommandWorkflow.saveConfigurationFiles()
String	CommandWorkflowModel.toXML()	Convert the object in XML.

Constructors in fr.ens.biologie.genomique.eoulsan.core.workflow that throw EoulsanException

Constructor	Description
AbstractWorkflow(ExecutorArguments executionArguments, Design design)	Protected constructor.
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, 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.
CommandWorkflow(ExecutorArguments executionArguments, CommandWorkflowModel workflowCommand, List<Module> firstSteps, List<Module> endSteps, Design design)	Public constructor.
Executor(ExecutorArguments arguments)	Constructor.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.data

Methods in fr.ens.biologie.genomique.eoulsan.data that throw EoulsanException

Modifier and Type	Method	Description
void	DataFormatRegistry.register(DataFormat df)	Register a DataFormat.
void	DataFormatRegistry.register(DataFormat[] array)	Register DataFormats.

Constructors in fr.ens.biologie.genomique.eoulsan.data that throw EoulsanException

Constructor	Description
XMLDataFormat(InputStream is, String source)	Public constructor.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.design

Methods in fr.ens.biologie.genomique.eoulsan.design that throw EoulsanException

Modifier and Type	Method	Description
void	DesignBuilder.addBcl2FastqSamplesheetProject(fr.ens.biologie.genomique.kenetre.illumina.samplesheet.SampleSheet samplesheet, String projectName, File bcl2fastqOutputDir)	Add all the sample from a Bclfastq samplesheet.
void	DesignBuilder.addBcl2FastqSamplesheetProject(File samplesheetFile, String projectName)	Add all the samples from a Bcl2Fastq samplesheet.
void	DesignBuilder.addFile(DataFile file)	Add a file to the design builder
void	DesignBuilder.addFile(String filename)	Add a filename to the design builder
void	DesignBuilder.addFiles(String[] filenames)	Add filenames to the design builder
void	DesignBuilder.addFiles(List<String> filenames)	Add filenames to the design builder
Design	DesignBuilder.getDesign(boolean pairedEndMode)	Create design object.
static Design	DesignUtils.readAndCheckDesign(InputStream is)	Read and Check design

Constructors in fr.ens.biologie.genomique.eoulsan.design that throw EoulsanException

Constructor	Description
DesignBuilder(String[] filenames)	Public constructor.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.galaxytools

Methods in fr.ens.biologie.genomique.eoulsan.galaxytools that return EoulsanException

Modifier and Type	Method	Description
static EoulsanException	GalaxyToolXMLParserUtils.newEoulsanException(ToolInfo toolInfo, String message)	Create an EoulsanException.
static EoulsanException	GalaxyToolXMLParserUtils.newEoulsanException(ToolInfo toolInfo, String parameterName, String message)	Create an EoulsanException.

Methods in fr.ens.biologie.genomique.eoulsan.galaxytools that throw EoulsanException

Modifier and Type	Method	Description
void	GalaxyToolInterpreter.configure(Set<Parameter> parameters)	Parse tool file to extract useful data to run tool.
String	CheetahInterpreter.execute()	Execute script by Python interpreter and replace variable name by value.
ToolExecutorResult	GalaxyToolInterpreter.execute(TaskContext context)	Convert command tag from tool file in string, variable are replace by value.
static Map<String,ToolElement>	GalaxyToolXMLParserUtils.extractConditionalParamElement(ToolInfo toolInfo, Element parent)	Extract conditional param element.
static Map<String,ToolElement>	GalaxyToolXMLParserUtils.extractConditionalParamElement(ToolInfo toolInfo, Element parent, Map<String,Parameter> stepParameters)	Extract conditional param element.
static List<Element>	GalaxyToolXMLParserUtils.extractElementsByTagName(ToolInfo toolInfo, Document doc, String tagName)	Extract elements by tag name.
static List<Element>	GalaxyToolXMLParserUtils.extractElementsByTagName(ToolInfo toolInfo, Document doc, String tagName, int expectedCount)	Extract elements by tag name.
static List<Element>	GalaxyToolXMLParserUtils.extractElementsByTagName(Element parent, String tagName)	Extract elements by tag name.
static List<Element>	GalaxyToolXMLParserUtils.extractElementsByTagName(Element parent, String tagName, int expectedCount)	Extract elements by tag name.
static Map<String,ToolElement>	GalaxyToolXMLParserUtils.extractInputs(ToolInfo toolInfo, Document doc, Map<String,Parameter> stepParameters)	Extract all input parameters define in document.
static Map<String,ToolElement>	GalaxyToolXMLParserUtils.extractOutputs(ToolInfo toolInfo, Document doc, Map<String,Parameter> stepParameters)	Extract all output parameters define in document.
static Map<String,ToolElement>	GalaxyToolXMLParserUtils.extractParamElement(ToolInfo toolInfo, Element parent, String elementName)	Extract parameter elements.
static Map<String,ToolElement>	GalaxyToolXMLParserUtils.extractParamElement(ToolInfo toolInfo, Element parent, String elementName, Map<String,Parameter> stepParameters)	Extract parameter elements.
static EoulsanException	GalaxyToolXMLParserUtils.newEoulsanException(ToolInfo toolInfo, String message)	Create an EoulsanException.
static EoulsanException	GalaxyToolXMLParserUtils.newEoulsanException(ToolInfo toolInfo, String parameterName, String message)	Create an EoulsanException.
static void	GalaxyToolXMLParserUtils.setElementValue(ToolElement toolElement, Map<String,Parameter> stepParameters)	Set the tool element value.

Constructors in fr.ens.biologie.genomique.eoulsan.galaxytools that throw EoulsanException

Constructor	Description
CheetahInterpreter(String cheetahScript, Map<String,String> variables)	Instantiates a new tool Cheetah script interpreter.
GalaxyToolInterpreter(File file)	Public constructor.
GalaxyToolInterpreter(InputStream in, String toolSource)	Public constructor.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.galaxytools.elements

Methods in fr.ens.biologie.genomique.eoulsan.galaxytools.elements that throw EoulsanException

Modifier and Type	Method	Description
static ToolElement	ToolElementFactory.newToolElement(ToolInfo toolInfo, Element param)	Gets the instance tool element.
static ToolElement	ToolElementFactory.newToolElement(ToolInfo toolInfo, Element tag, String nameSpace)	Gets the instance tool element.
void	BooleanParameterToolElement.setValue(String value)
void	FloatParameterToolElement.setValue(String value)
void	IntegerParameterToolElement.setValue(String value)
void	SelectParameterToolElement.setValue(String value)
void	TextParameterToolElement.setValue(String value)
void	ToolElement.setValue(String value)	Sets the value.
void	ConditionalToolElement.setValues(Map<String,Parameter> stepParameters)	Set the values.

Constructors in fr.ens.biologie.genomique.eoulsan.galaxytools.elements that throw EoulsanException

Constructor	Description
ConditionalToolElement(ToolInfo toolInfo, Element element)	Instantiates a new tool conditional element.
DataToolElement(ToolInfo toolInfo, Element param, String nameSpace)	Instantiates a new tool outputs data.
FloatParameterToolElement(ToolInfo toolInfo, Element param)	Instantiates a new float tool parameter.
FloatParameterToolElement(ToolInfo toolInfo, Element param, String nameSpace)	Instantiates a new float tool parameter.
IntegerParameterToolElement(ToolInfo toolInfo, Element param)	Instantiates a new integer tool element parameter.
IntegerParameterToolElement(ToolInfo toolInfo, Element param, String nameSpace)	Instantiates a new integer tool element parameter.
SelectParameterToolElement(ToolInfo toolInfo, Element param)	Instantiates a new select tool element parameter.
SelectParameterToolElement(ToolInfo toolInfo, Element param, String nameSpace)	Instantiates a new select tool element parameter.
TextParameterToolElement(ToolInfo toolInfo, Element param)	Instantiates a new text tool element parameter.
TextParameterToolElement(ToolInfo toolInfo, Element param, String nameSpace)	Instantiates a new text tool element parameter.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules

Methods in fr.ens.biologie.genomique.eoulsan.modules that throw EoulsanException

Modifier and Type	Method	Description
void	AbstractModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	CopyInputDataModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	CopyOutputDataModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	DesignModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	FailModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	GalaxyToolModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	ImportModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	MergerModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	RequirementInstallerModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	ShellModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	SplitterModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Constructors in fr.ens.biologie.genomique.eoulsan.modules that throw EoulsanException

Constructor	Description
GalaxyToolModule(InputStream toolXMLis)	Constructor.
GalaxyToolModule(InputStream in, String source)	Constructor.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules.chipseq

Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq that throw EoulsanException

Modifier and Type	Method	Description
void	MergeInputRepLocalModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	RmDupLocalModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	TrackHubModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling

Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling that throw EoulsanException

Modifier and Type	Method	Description
void	BedToolsModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	DeepToolsModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	MACS2Module.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc

Methods in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc that throw EoulsanException

Modifier and Type	Method	Description
void	CountSplicedReadsModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set the parameters of the step to configure the step.
void	IDRModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)	Set IDR parameters to configure the step.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules.diffana

Methods in fr.ens.biologie.genomique.eoulsan.modules.diffana that throw EoulsanException

Modifier and Type	Method	Description
protected void	Normalization.checkRepTechGroupCoherence(List<String> rRepTechGroup, List<String> rCondNames)	Check if there is a problem in the repTechGroup coherence.
void	DESeq2Module.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	DiffAnaModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	DiffanaResultsAnnotationModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	NormalizationModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
protected String	DiffAna.generateScript(Experiment experiment, TaskContext context)
protected String	Normalization.generateScript(Experiment experiment, TaskContext context)	Generate the R script.
static DESeq2.FitType	DESeq2.FitType.get(String name)	Get the fit type to be used in DESeq2.
static DESeq2.SizeFactorsType	DESeq2.SizeFactorsType.get(Parameter parameter)	Get the size factors type to be used in DESeq2.
static DESeq2.StatisticTest	DESeq2.StatisticTest.get(String name)	Get the statistic test to be used in DESeq2.
static RExecutor	RModuleCommonConfiguration.parseRExecutorParameter(StepConfigurationContext context, Set<Parameter> stepParameters, Set<Requirement> requirements, String defaultDockerImage)	Parse the step parameter and create a configured RExecutor object.
protected String	Normalization.readStaticScript(String staticFile)	Read a static part of the generated script.
void	Normalization.run(TaskContext context, Data data)	Run normalisation step
void	DESeq2.runDEseq2(DataFile workflowOutputDir)	Method to run DESeq2.
protected void	Normalization.runRExecutor(TaskContext context, Data data)	Execute Rnw script.

Constructors in fr.ens.biologie.genomique.eoulsan.modules.diffana that throw EoulsanException

Constructor	Description
DiffAna(RExecutor executor, Design design, DiffAna.DispersionMethod dispEstMethod, DiffAna.DispersionSharingMode dispEstSharingMode, DiffAna.DispersionFitType dispEstFitType)	Public constructor.
Normalization(RExecutor executor, Design design)	Public constructor.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules.expression

Methods in fr.ens.biologie.genomique.eoulsan.modules.expression that throw EoulsanException

Modifier and Type	Method	Description
void	AbstractExpressionModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	ExpressionResultsAnnotationModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop

Methods in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop that throw EoulsanException

Modifier and Type	Method	Description
void	ExpressionHadoopModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules.fastqc

Methods in fr.ens.biologie.genomique.eoulsan.modules.fastqc that throw EoulsanException

Modifier and Type	Method	Description
void	FastQCModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
static void	FastQCRuntimePatcher.patchFastQC()	Patch FastQC for hadoop mode.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules.generators

Methods in fr.ens.biologie.genomique.eoulsan.modules.generators that throw EoulsanException

Modifier and Type	Method	Description
void	GenericStorageGeneratorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	GenomeMapperIndexGeneratorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	Minimap2IndexGeneratorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	STARIndexGeneratorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules.mapping

Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping that throw EoulsanException

Modifier and Type	Method	Description
void	AbstractBAM2SAMModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractFilterAndMapReadsModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractReadsFilterModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractReadsMapperModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractSAM2BAMModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractSAM2FASTQModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractSAMFilterModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	AbstractSplice2BEDModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
protected fr.ens.biologie.genomique.kenetre.bio.alignmentfilter.MultiReadAlignmentFilter	AbstractSAMFilterModule.getAlignmentFilter(fr.ens.biologie.genomique.kenetre.log.GenericLogger logger, fr.ens.biologie.genomique.kenetre.util.ReporterIncrementer incrementer, String counterGroup)	Get the ReadAlignmentsFilter object.
protected fr.ens.biologie.genomique.kenetre.bio.readfilter.MultiReadFilter	AbstractReadsFilterModule.getReadFilter(fr.ens.biologie.genomique.kenetre.log.GenericLogger logger, fr.ens.biologie.genomique.kenetre.util.ReporterIncrementer incrementer, String counterGroup)	Get the ReadFilter object.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop

Methods in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop that throw EoulsanException

Modifier and Type	Method	Description
void	FilterAndMapReadsHadoopModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	ReadsMapperHadoopModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop

Methods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop that throw EoulsanException

Modifier and Type	Method	Description
void	CopyDesignAndWorkflowFilesToOutputModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	DistCp.runWithException(String[] args)	This is the main driver for recursively copying directories across file systems.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload

Methods in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload that throw EoulsanException

Modifier and Type	Method	Description
void	DefineDataFormatToDownload.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	HDFSDataDownloadModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules.multiqc

Methods in fr.ens.biologie.genomique.eoulsan.modules.multiqc that throw EoulsanException

Modifier and Type	Method	Description
void	MultiQCModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.modules.singlecell

Methods in fr.ens.biologie.genomique.eoulsan.modules.singlecell that throw EoulsanException

Modifier and Type	Method	Description
void	ExpressionToMatrixModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	MatrixToCellRangerMatrixModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)
void	RSingleCellExperimentCreatorModule.configure(StepConfigurationContext context, Set<Parameter> stepParameters)

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.requirements

Methods in fr.ens.biologie.genomique.eoulsan.requirements that throw EoulsanException

Modifier and Type	Method	Description
void	AbstractRequirement.configure(Set<Parameter> parameters)
void	DockerRequirement.configure(Set<Parameter> parameters)
void	PathRequirement.configure(Set<Parameter> parameters)
void	Requirement.configure(Set<Parameter> parameters)	Configure the requirement.
void	RserveRequirement.configure(Set<Parameter> parameters)
void	DockerRequirement.install(Progress progress)
void	PathRequirement.install(Progress progress)
void	Requirement.install(Progress progress)	Install the requirement.
void	RserveRequirement.install(Progress progress)
static Requirement	DockerRequirement.newDockerRequirement(String dockerImage)	Create a new docker image as mandatory requirement.
static Requirement	DockerRequirement.newDockerRequirement(String dockerImage, boolean optional)	Create a new docker image requirement.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.splitermergers

Methods in fr.ens.biologie.genomique.eoulsan.splitermergers that throw EoulsanException

Modifier and Type	Method	Description
void	BAMMerger.configure(Set<Parameter> conf)
void	BAMSplitter.configure(Set<Parameter> conf)
void	ExpressionMerger.configure(Set<Parameter> conf)
void	ExpressionSplitter.configure(Set<Parameter> conf)
void	FastqMerger.configure(Set<Parameter> conf)
void	FastqSplitter.configure(Set<Parameter> conf)
void	Merger.configure(Set<Parameter> conf)	Configure the merger.
void	SAMMerger.configure(Set<Parameter> conf)
void	SAMSplitter.configure(Set<Parameter> conf)
void	Splitter.configure(Set<Parameter> conf)	Configure the splitter.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.util

Methods in fr.ens.biologie.genomique.eoulsan.util that throw EoulsanException

Modifier and Type	Method	Description
protected abstract S	AbstractResourceLoader.load(InputStream in, String source)	Load a resource.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.util.hadoop

Methods in fr.ens.biologie.genomique.eoulsan.util.hadoop that throw EoulsanException

Modifier and Type	Method	Description
static void	MapReduceUtils.submitAndWaitForJob(org.apache.hadoop.mapreduce.Job job, String jobDescription, int waitTimeInMillis, TaskStatus status, String counterGroup)	Wait the completion of a job.

Uses of EoulsanException in fr.ens.biologie.genomique.eoulsan.util.locker

Methods in fr.ens.biologie.genomique.eoulsan.util.locker that throw EoulsanException

Modifier and Type	Method	Description
boolean	DistributedLock.tryLock(long timeout, TimeUnit unit)