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A

ABORTED - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
 
ABOUT_TXT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
About string, plain text version.
AbstractAction - Class in fr.ens.biologie.genomique.eoulsan.actions
This class define an abstract Action
AbstractAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.AbstractAction
 
AbstractBAM2SAMModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping
This class define a module for converting BAM files into SAM.
AbstractBAM2SAMModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
 
AbstractClusterTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This class is a scheduler for task running on a cluster.
AbstractClusterTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler
 
AbstractClusterTaskScheduler.ProcessThreadOutput - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This class allow to fetch standard output or standard error.
AbstractConcatInputStream - Class in fr.ens.biologie.genomique.eoulsan.io
This class define an InputStream that concatenate InputStream.
AbstractConcatInputStream() - Constructor for class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
 
AbstractEoulsanRuntime - Class in fr.ens.biologie.genomique.eoulsan
This class define an abstract EoulsanRuntime.
AbstractEoulsanRuntime(Settings) - Constructor for class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
 
AbstractEoulsanRuntime.EoulsanExecMode - Enum in fr.ens.biologie.genomique.eoulsan
This Enum define the Eoulsan execution mode.
AbstractExecutorInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters
This class define an abstract executor interpreter that contains the default implementation of the execute() method that use a ProcessBuilder.
AbstractExecutorInterpreter() - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.AbstractExecutorInterpreter
 
AbstractExpressionModule - Class in fr.ens.biologie.genomique.eoulsan.modules.expression
This abstract class define and parse arguments for the expression module.
AbstractExpressionModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
 
AbstractFilterAndMapReadsModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping
This class define an abstract module for read filtering, mapping and alignments filtering.
AbstractFilterAndMapReadsModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
 
AbstractInfoAction - Class in fr.ens.biologie.genomique.eoulsan.actions
This class define an abstract action that show the some Eoulsan configuration and available modules
AbstractInfoAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.AbstractInfoAction
 
AbstractMetadata - Class in fr.ens.biologie.genomique.eoulsan.design
This abstract class defines methods for metadata.
AbstractMetadata() - Constructor for class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
AbstractModule - Class in fr.ens.biologie.genomique.eoulsan.modules
This class define an abstract Module.
AbstractModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
 
AbstractParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements
This class define an abstract class for tool element parameters.
AbstractParameterToolElement(Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractParameterToolElement
Protected constructor.
AbstractPort - Class in fr.ens.biologie.genomique.eoulsan.core
Abstract class that define a port.
AbstractPorts<E extends Port> - Class in fr.ens.biologie.genomique.eoulsan.core
This class define a basic implementation of a Ports class.
AbstractPorts(Set<E>) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
Constructor.
AbstractReadsFilterModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping
This class define an abstract module for read filtering.
AbstractReadsFilterModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
 
AbstractReadsMapperModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping
This class define an abstract module for read mapping.
AbstractReadsMapperModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
AbstractRequirement - Class in fr.ens.biologie.genomique.eoulsan.requirements
This class define an abstract requirement.
AbstractRequirement() - Constructor for class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
 
AbstractResourceLoader<S> - Class in fr.ens.biologie.genomique.eoulsan.util
This class define an abstract resource loader.
AbstractResourceLoader() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader
 
AbstractRExecutor - Class in fr.ens.biologie.genomique.eoulsan.util.r
This class define an abstract RExecutor.
AbstractRExecutor(File, File) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
Constructor.
AbstractSAM2BAMModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping
This class define a module for converting SAM files into BAM.
AbstractSAM2BAMModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
 
AbstractSAM2FASTQModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping
This class define a module for converting SAM files into BAM.
AbstractSAM2FASTQModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
 
AbstractSAMFilterModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping
This class define an abstract module for alignments filtering.
AbstractSAMFilterModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
 
AbstractSplice2BEDModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping
This class define a module for converting SAM files into BED.
AbstractSplice2BEDModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
 
AbstractStep - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a step of the workflow.
AbstractTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers
This class define an abstract task scheduler.
AbstractTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
Protected constructor.
AbstractToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements
This class define an abstract tool element.
AbstractToolElement(Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
Instantiates a new abstract tool element.
AbstractToolElement(Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
Instantiates a new abstract tool element.
AbstractWorkflow - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a Workflow.
AbstractWorkflow(ExecutorArguments, Design) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
Protected constructor.
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ActionService
 
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskSchedulerService
 
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleService
 
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
 
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessorService
 
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RequirementService
 
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.ui.UIService
 
accept(Class<?>, boolean) - Static method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
Check that annotation of a class is compatible with the Eoulsan mode (local or Hadoop).
accept(Path) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils.PrefixPathFilter
 
accept(Path) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils.SuffixPathFilter
 
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractInfoAction
 
action(List<String>) - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action
Execute action.
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction
 
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
 
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
 
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
 
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecAction
 
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
 
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction
 
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.IntegrationTestAction
 
Action - Interface in fr.ens.biologie.genomique.eoulsan.actions
This interface define an action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction
Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ExecAction
Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.FormatsAction
Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction
Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.InfoAction
Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ModulesAction
Name of this action.
ActionService - Class in fr.ens.biologie.genomique.eoulsan.actions
This class define a service to retrieve an Action
ActionService() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ActionService
Private constructor.
add(EmergencyStopTask) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.EmergencyStopTasks
Add an emergency task.
add(String, Object) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore
Store some data.
addBcl2FastqSamplesheetProject(SampleSheet, String, File) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder
Add all the sample from a Bclfastq samplesheet.
addBcl2FastqSamplesheetProject(File, String) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder
Add all the samples from a Bcl2Fastq samplesheet.
addConstant(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Add a constant.
addConstant(String, String, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Add a constant.
addConstants(ExecutorArguments) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Add job arguments information to constants.
addDataToList(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
 
addDataToList(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
addDataToList(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Add a data to the list of data.
addDataToList(String, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
 
addDataToList(String, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
addDataToList(String, int) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Add a data to the list of data.
addDependency(AbstractStep) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
Add a dependency for this step.
addDependency(AbstractStep) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies
Add a dependency.
addDependency(StepInputPort, StepOutputPort) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
Add a dependency for this step.
addExperiment(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Add an experiment.
addFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder
Add a file to the design builder
addFile(File, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.JarRepack
Add a file to the jar file.
addFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder
Add a filename to the design builder
addFiles(String[]) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder
Add filenames to the design builder
addFiles(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder
Add filenames to the design builder
addHadoopJobEmergencyStopTask(ClusterTaskScheduler, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask
Add a cluster Job to the EmergencyStopTasks.
addHadoopJobEmergencyStopTask(Job) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJobEmergencyStopTask
Add an Hadoop Job to the EmergencyStopTasks.
addHandler(Handler) - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler
Add an Handler.
ADDITIONAL_ANNOTATION_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
 
ADDITIONAL_ANNOTATION_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Additional annotation data format.
AdditionalAnnotationDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define a additional annotation protocol.
AdditionalAnnotationDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.AdditionalAnnotationDataProtocol
 
additionalScriptEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
Define additional environment variable for bpipe scripts.
additionalScriptEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.HTCondorTaskScheduler
 
addObserver(StepObserver) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry
Add a listener.
addPort(String, boolean, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Add an input port.
addPort(String, boolean, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder
Add an output port.
addPort(String, boolean, DataFormat, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Add an input port.
addPort(String, boolean, DataFormat, CompressionType) - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder
Add an output port.
addPort(String, boolean, DataFormat, EnumSet<CompressionType>) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Add an input port.
addPort(String, boolean, DataFormat, EnumSet<CompressionType>, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Add an input port.
addPort(String, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Add an input port.
addPort(String, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder
Add an output port.
addPort(String, DataFormat, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Add an input port.
addPort(String, DataFormat, CompressionType) - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder
Add an output port.
addPort(String, DataFormat, EnumSet<CompressionType>) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Add an input port.
addPort(String, DataFormat, EnumSet<CompressionType>, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Add an input port.
addResource(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader
Add a resource.
addResourcePath(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader
Add a resource path.
addResourcePaths(Collection<String>) - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader
Add a resource paths.
addResult(TaskContextImpl, TaskResultImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Add a task result to the step result.
addSample(Sample) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment
Add a sample.
addSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
addSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
addSample(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Add a sample.
afterExecute(Runnable, Throwable) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.PausableThreadPoolExecutor
 
afterExecuteTask(TaskContextImpl, TaskResultImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
Set the state of the context after executing a task.
ALIGNMENTS_REJECTED_BY_FILTERS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
ALIGNMENTS_WITH_INVALID_SAM_FORMAT - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
ALIGNMENTS_WITH_MORE_ONE_HIT_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
allPortsRequiredInWorkingDirectory(InputPorts) - Static method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Set all ports of an existing input ports to be required in working directory.
AMAZON - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
 
AMBIGUOUS_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
ANNOTATED_EXPRESSION_RESULTS_ODS - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
ODS Annotated expression results data format.
ANNOTATED_EXPRESSION_RESULTS_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
TSV Annotated expression results data format.
ANNOTATED_EXPRESSION_RESULTS_XLSX - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
XLSX Annotated expression results data format.
ANNOTATION_GFF - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
GFF data format.
ANNOTATION_GTF - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
GTF data format.
AnnotationDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define a annotation protocol.
AnnotationDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.AnnotationDataProtocol
 
ANY_VERSION - Static variable in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock
The magic version number that allows any mutation to always succeed regardless of actual version number.
ApacheCommonCompressionCodecs - Class in fr.ens.biologie.genomique.eoulsan.io
This class allow to create input and output stream for compression codecs of the Apache Common Compression library.
ApacheCommonCompressionCodecs() - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ApacheCommonCompressionCodecs
 
APP_BUILD_COMMIT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
The built commit of the application.
APP_BUILD_DATE - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
The build date of the application.
APP_BUILD_HOST - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
The built host of the application.
APP_BUILD_NUMBER - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
The built number of the application.
APP_BUILD_YEAR - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
The build year of the application.
APP_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
The name of the application.
APP_NAME_LOWER_CASE - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
The name of the application.
APP_VERSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
The version of the application.
APP_VERSION_STRING - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
The version of the application.
ASAP - fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput
 
ASCII_CHARSET - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets
Ascii charset.
ASCII_ENCODING - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets
Ascii file encoding.
ASCII_LETTER_OR_DIGIT - Static variable in class fr.ens.biologie.genomique.eoulsan.core.Naming
 
AVAILABLE_BINARY_ARCH - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Platforms where the application is available.
AVAILABLE_BINARY_ARCH_ALIAS - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Platforms alias.
AVAILABLE_PROCESSORS_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Available processor constant name.
AWS_S3_ACCESS_KEY_ID_PARAM_KEY - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
 
AWS_S3_SECRET_ACCESS_KEY_PARAM_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
 

B

badParameterValue(StepConfigurationContext, Parameter, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Throw a exception for bad parameter value.
badParameterValue(String, Parameter, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Throw a exception for bad parameter value.
BAM2SAMLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local
This class define a module for converting BAM files into SAM.
BAM2SAMLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.BAM2SAMLocalModule
 
BAMMerger - Class in fr.ens.biologie.genomique.eoulsan.splitermergers
This class define a merger class for SAM files.
BAMMerger() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMMerger
 
BAMSplitter - Class in fr.ens.biologie.genomique.eoulsan.splitermergers
This class define a splitter class for BAM files.
BAMSplitter() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMSplitter
 
base64ForIcon(String, Class) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCRuntimePatcher
This method replace the HTMLReportArchive.base64ForIcon() method.
BasicUI - Class in fr.ens.biologie.genomique.eoulsan.ui
This class define a basic UI for Eoulsan.
BasicUI() - Constructor for class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
 
BedToolsModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling
This class uses tools from the BEDTools suite.
BedToolsModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
 
beforeExecute(Thread, Runnable) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.PausableThreadPoolExecutor
 
beforeExecuteTask(TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
Set the state of the context before executing a task.
BIGBED - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
BigBed format.
BIGWIG - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
BigWig format.
BLIND - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod
 
BooleanParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements
This class define a boolean tool element parameter.
BooleanParameterToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement
Instantiates a new boolean tool parameter.
BooleanParameterToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement
Instantiates a new boolean tool parameter.
BOWTIE_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Bowtie index data format.
BOWTIE2_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Bowtie2 index data format.
BpipeTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This class allow to submit, stop and get the status of jobs using Bpipe scheduler wrappers.
BpipeTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
 
BufferedHandler - Class in fr.ens.biologie.genomique.eoulsan
This class define a buffered handler.
BufferedHandler() - Constructor for class fr.ens.biologie.genomique.eoulsan.BufferedHandler
 
BUILD_CONTRAST_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
 
BUILD_DATE_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Build date constant name.
BUILD_NUMBER_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Build number constant name.
BundledScriptBpipeTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This class define an abstract scheduler that use a bpipe script bundled in Eoulsan distribution.
BundledScriptBpipeTaskScheduler(String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BundledScriptBpipeTaskScheduler
Constructor.
BWA_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
BWA index data format.
BYPASS_PLATFORM_CHECKING - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Bypass platform checking.
ByteCountInputStream - Class in fr.ens.biologie.genomique.eoulsan.io
This filter class allow to count the number of bytes read by an inputStream.
ByteCountInputStream(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
Public constructor
ByteCountInputStream(InputStream, long) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
Public constructor
ByteCountOutputStream - Class in fr.ens.biologie.genomique.eoulsan.io
This class define a filter that count the number of written bytes by an InputStream.
ByteCountOutputStream(OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream
Public constructor.
ByteCountOutputStream(OutputStream, long) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream
Public constructor.

C

CALL_METHOD - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter
The Constant CALL_METHOD.
canDelete() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Test if the delete() method is available with this protocol.
canDelete() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
canDelete() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
 
canList() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Test if the list() method is available with this protocol.
canList() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
canList() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
 
canMkdir() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Test if the mkdir() and mkdirs() methods are available with this protocol.
canMkdir() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
canMkdir() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
 
canonicalize() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
canRead() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Test if source is readable with this protocol.
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
 
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
 
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
 
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
 
canRename() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Test if the renameTo() method is available with this protocol.
canRename() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
canRename() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
 
canSymlink() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Test if the symlink() method is available with this protocol.
canSymlink() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
canWrite() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Test if source is writable with this protocol.
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
 
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
 
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
 
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
 
changeFileExtension(File, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
Change the extendsion of a file
check(Data, CheckStore) - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker
Launch the check.
check(Data, CheckStore) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
 
check(Data, CheckStore) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
 
check(Data, CheckStore) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
 
check(Data, CheckStore) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
 
CHECK_COMPLETION_TIME - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
 
checkAnnotations(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Check if there is more than one annotation in the design
checkDirectories() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
Check directories needed by the workflow.
Checker - Interface in fr.ens.biologie.genomique.eoulsan.checkers
This interface define a checker.
CHECKER_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
 
CheckerModule - Class in fr.ens.biologie.genomique.eoulsan.modules
This class is a module that launch checkers.
CheckerModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
Public constructor.
checkExistingDirectoryFile(Path, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Check if a directory exists
checkExistingFile(Path, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Check if a file exists
checkExistingStandardFile(Path, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Check if a file exists
checkExistingStandardFileOrDirectory(Path, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Check if a file exists
checkExperimentDesign(Experiment) - Static method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
Check experiment design.
checkForPartDuplicates() - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
 
checkForPartDuplicates() - Method in class fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule
 
checkGenomes(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Check if there is more than one genome in the design
checkOutputSpecs(JobContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.CLIMergingAnySAMOutputFormat
 
checkRepTechGroupCoherence(List<String>, List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Check if there is a problem in the repTechGroup coherence.
checkSamples(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Check if there are duplicate samples in the design.
CheckStore - Class in fr.ens.biologie.genomique.eoulsan.checkers
This class define a storage where some results of the checker can be save for later reuse by other checkers.
CheetahInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools
This class create a Cheetah interpreter, it can build a command line tool from command tag from Galaxy tool XML file.
CheetahInterpreter(String, Map<String, String>) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter
Instantiates a new tool Cheetah script interpreter.
ChIPSeqDataFormats - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq
This class contains the definition of some DataFormats for ChiP-Seq.
ClassLoaderObjectInputStream - Class in fr.ens.biologie.genomique.eoulsan.util
This class allow to use ObjectInputStream with a ClassLoader that is not the default bootstrap ClassLoader.
ClassLoaderObjectInputStream(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.ClassLoaderObjectInputStream
Constructor, use the thread ClassLoader to load classes of objects to instantiate.
ClassLoaderObjectInputStream(ClassLoader, InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.ClassLoaderObjectInputStream
Constructor.
ClassPathResourceLoader<S> - Class in fr.ens.biologie.genomique.eoulsan.util
This class allow to define a resource loader for resources in the class path.
ClassPathResourceLoader(Class<S>, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.ClassPathResourceLoader
Constructor.
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionMapper
 
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentMapper
 
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionMapper
 
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionSAMOutputMapper
 
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterMapper
 
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperMapper
 
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterMapper
 
cleanupJob(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
 
cleanupJob(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler
Cleanup after a job.
clear() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore
Clear the content of the CheckStore.
clear() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Clear the entries of the object.
CLIMergingAnySAMOutputFormat<K> - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli
 
CLIMergingAnySAMOutputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.CLIMergingAnySAMOutputFormat
 
close() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
 
close() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
 
close() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
 
close() - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler
 
close() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.DesignFormatFinderInputStream
 
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
 
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
 
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream
 
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.MaxByteInputStream
 
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterInputStream
 
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterOutputStream
 
close() - Method in class fr.ens.biologie.genomique.eoulsan.util.JarRepack
Close the repackaged file.
close(JobContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils.SAMHeaderWriter
Close the SAM file header.
close(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.ExpressionRecordWriter
 
close(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordWriter
 
close(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordWriter
 
closeConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
 
closeConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
 
closeConnection() - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor
Close the connection.
closeConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
 
cloudInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with cloud configuration informations.
CLUSTER - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
 
CLUSTER_TASK - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
 
ClusterCombinedTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers
This class defined a combined task scheduler for cluster mode.
ClusterCombinedTaskScheduler(int, ClusterTaskScheduler) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
Constructor.
ClusterExecAction - Class in fr.ens.biologie.genomique.eoulsan.actions
This class define the cluster exec Action.
ClusterExecAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction
 
clusterInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with cluster configuration informations.
ClusterJobEmergencyStopTask - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This class define an EmergencyStopTask for cluster Jobs.
ClusterJobEmergencyStopTask(ClusterTaskScheduler, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask
Public constructor.
ClusterTaskAction - Class in fr.ens.biologie.genomique.eoulsan.actions
This class define a action to launch a task on a cluster.
ClusterTaskAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
 
ClusterTaskScheduler - Interface in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This interface define a cluster task scheduler.
ClusterTaskScheduler.StatusResult - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This class define a Status result return by the statusJob() method of the interface.
ClusterTaskScheduler.StatusValue - Enum in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This enum define the values of the status of a job.
ClusterTaskSchedulerService - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This class define a service to retrieve a ClusterTaskScheduler.
CollectionUtils - Class in fr.ens.biologie.genomique.eoulsan.util
This class define an utility class that contains useful methods for collections.
CombinedTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers
This class defined a combined task scheduler that use several context schedulers according to the parallelization mode of the step.
CombinedTaskScheduler(int) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
Constructor.
COMMA - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
SPLITTER.
commandLineInfo(Main) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with command line informations.
CommandStep - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a step based on a Command object (workflow file).
CommandStep(AbstractWorkflow, Module) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep
Create a step for a standard step from an existing step object.
CommandStep(AbstractWorkflow, Module, Set<Parameter>) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep
Create a step for a standard step from an existing step object.
CommandStep(AbstractWorkflow, Step.StepType) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep
Constructor that create a step with nothing to execute like ROOT_STEP, DESIGN_STEP and FIRST_STEP.
CommandStep(AbstractWorkflow, DataFormat) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep
Create a Generator Workflow step.
CommandStep(AbstractWorkflow, String, String, String, Set<Parameter>, boolean, Step.DiscardOutput, int, int, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep
Create a step for a standard step.
CommandStep(AbstractWorkflow, String, String, String, Set<Parameter>, boolean, Step.DiscardOutput, int, int, String, DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep
Create a step for a standard step.
CommandWorkflow - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a workflow based on a Command object (workflow file).
CommandWorkflow(ExecutorArguments, CommandWorkflowModel, List<Module>, List<Module>, Design) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflow
Public constructor.
CommandWorkflowModel - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define the workflow model object of Eoulsan.
CommandWorkflowModel() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Public constructor.
CommandWorkflowModel(boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Public constructor.
CommandWorkflowParser - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class allow parse the workflow file.
CommandWorkflowParser(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Public constructor.
CommandWorkflowParser(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Public constructor.
CommandWorkflowParser(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Public constructor.
CommandWorkflowParser.StepOutputPort - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
 
COMMENT_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
 
Common - Class in fr.ens.biologie.genomique.eoulsan
This class define common constants.
CommonHadoop - Class in fr.ens.biologie.genomique.eoulsan
This class define common constants and other methods specific to Hadoop mode.
CommonHadoop() - Constructor for class fr.ens.biologie.genomique.eoulsan.CommonHadoop
 
compareTo(Parameter) - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
 
compareTo(StepOutputDataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
 
compareTo(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
 
compareTo(DataFileDataPath) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
compareTo(Ticket) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
COMPARISONS_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
 
compatibilityFilename() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Return the filename using Eoulsan 1.x naming.
COMPLETE - fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusValue
 
CompressedSplitFastqLineReader - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
 
CompressedSplitFastqLineReader(SplitCompressionInputStream, Configuration, byte[]) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.CompressedSplitFastqLineReader
 
computeMD5Sum(DataPath) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeDescStorage
 
concat(List<Path>, Path, boolean, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Copy all files in a directory to one output file (merge).
concat(List<Path>, Path, boolean, boolean, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Copy all files in a directory to one output file (merge).
concat(List<Path>, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Copy all files in a directory to one output file (merge).
CONDITION_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
 
CONDITION_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
 
ConditionalToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements
This class define a conditional tool element.
ConditionalToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
Instantiates a new tool conditional element.
conf - Variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
 
configure() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
Configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module
Set the parameters of the step to configure the module.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule
Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule
Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule
Set IDR parameters to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule
Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.FilterAndMapReadsHadoopModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperHadoopModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
 
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
 
configure(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
 
configure(Settings) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler
Configure the scheduler.
configure(Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker
Set the parameters of the checker to configure the checker.
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
 
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
 
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
 
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
 
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter
Parse tool file to extract useful data to run tool.
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
 
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
 
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
 
configure(Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement
Configure the requirement.
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
 
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMMerger
 
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMSplitter
 
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionMerger
 
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionSplitter
 
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqMerger
 
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqSplitter
 
configure(Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Merger
Configure the merger.
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMMerger
 
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMSplitter
 
configure(Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Splitter
Configure the splitter.
configureChecker(DataFormat, Set<Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
This method allow to configure a checker from the configure method of other steps, that's why this method is static.
CONFIGURED - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
 
configureLog4J(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.OtherLogConfigurator
Configure Log4J.
configureSampling(Path, String, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
 
CONTACT_EMAIL - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Project email.
contains(E) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
 
contains(E) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports
Test if a port exists by testing if port name exists.
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore
Test if a data exists.
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
 
contains(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports
Test if a port exists.
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
contains(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
Test if the key is in md.
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
containsAdditionalAnnotationFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
Test if the additional annotation file field exists.
containsAdditionalAnnotationFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
 
containsBuildContrast() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Test if the buildContrast option exists.
containsBuildContrast() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
containsComment() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Test if the comment field exists.
containsComparisons() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Test if the comparisons option exists.
containsComparisons() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
containsCondition() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
Test if the condition field exists.
containsCondition() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
 
containsCondition() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Test if the condition field exists.
containsCondition() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
containsContrast() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Test if the contrast option exists.
containsContrast() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
containsContrastFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Test if the contrastFile option exists.
containsContrastFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
containsDate() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Test if the date field exists.
containsDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Test if the description field exists.
containsDesignFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Test if the designFile option exists.
containsDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
containsExperiment(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Test if the experiment exists.
containsExperimentName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
 
containsFastqFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Test if the fastq format field exists.
containsGenomeFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
Test if the genomeFile field exists.
containsGenomeFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
 
containsGffFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
Test if the gffFile field exists.
containsGffFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
 
containsGtfFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
Test if the gtfFile field exists.
containsGtfFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
 
containsKey(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Test if a key exists.
containsModel() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Test if the model option exists.
containsModel() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
containsOperator() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Test if the operator field exists.
containsParameter(Set<Parameter>, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
test if a set of parameters contains a parameter.
containsReads() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Test if the reads field exists.
containsReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Test if the reference option exists.
containsReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
Test if the reference field exists.
containsReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
 
containsReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Test if the reference field exists.
containsReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
containsReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
containsReferenceField(Experiment) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Test if an experiment contains reference fields
containsRepTechGroup() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
Test if the RepTechGroup field exists.
containsRepTechGroup() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
 
containsRepTechGroup() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Test if the RepTechGroup field exists.
containsRepTechGroup() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
containsSample(Sample) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment
Test if the experiment contains a sample.
containsSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
containsSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
containsSample(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Test if the sample exists.
containsSampleName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
 
containsSerialNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Test if the serial number field exists.
containsSkip() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Test if the skip option exists.
containsSkip() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
containsUUID() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Test if the UUID field exists.
ContextUtil - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli
Utility methods to allow applications to deal with inconsistencies between MapReduce Context Objects API between hadoop-0.20 and later versions.
ContextUtil() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil
 
ContextUtils - Class in fr.ens.biologie.genomique.eoulsan.core
This class define utility methods on Context.
CONTRAST_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
 
CONTRAST_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
 
convert() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatConverter
 
convert(Configuration, DataFile, DataFile, DataFile, int) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PairedEndFastqToTfq
Create the job to convert FASTQ files in a TFQ file.
convert(Configuration, Path, Path, Path, int) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PairedEndFastqToTfq
Create the job to convert FASTQ files in a TFQ file.
copy(InputPorts) - Static method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Convenient method to create a defensive copy of an InputPorts object.
copy(OutputPorts) - Static method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder
Convenient method to create a defensive copy of an OutputPorts object.
copy(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.data.DataFiles
Copy a file, if input data is compressed, data will be uncompressed and if output require to be compressed output will be compressed.
copy(DataPath) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
copy(Map<DataFile, DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DataFileDistCp
 
copy(Map<DataFile, DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HadoopUploadModule
 
copy(Map<DataFile, DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.LocalUploadModule
 
copy(Map<DataFile, DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
Copy files to destinations.
copy(Configuration, String, String, Path, boolean, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp
Deprecated.
copy(Path, Path, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Copy file from a path to another path.
copy(Path, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Copy file from a path to another path.
copyAndCompressInputStreamToPath(InputStream, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Copy bytes from an InputStream to a path.
copyAndCompressLocalFileToPath(File, Path, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Copy a local file to a path
copyAndCompressLocalFileToPath(File, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Copy a local file to a path
CopyDesignAndWorkflowFilesToOutputModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop
This module copy design and workflow file to output directory.
CopyDesignAndWorkflowFilesToOutputModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
 
copyFromPathToLocalFile(Path, File, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Copy a file from a path to a local file
copyFromPathToLocalFile(Path, File, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Copy a file from a path to a local file.
CopyInputDataModule - Class in fr.ens.biologie.genomique.eoulsan.modules
Copy input files of a format in another location or in different compression format.
CopyInputDataModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
 
copyInputStreamToPath(InputStream, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Copy bytes from an InputStream to a path.
copyLocalFileToPath(File, Path, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Copy a local file to a path
copyLocalFileToPath(File, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Copy a local file to a path
copyMerge(Path, Path, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Merge several file of a directory into one file.
copyMerge(Path, Path, boolean, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Merge several file of a directory into one file.
copyMerge(Path, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Merge several file of a directory into one file.
CopyOutputDataModule - Class in fr.ens.biologie.genomique.eoulsan.modules
Copy output files of a step with a specified format to the output directory.
CopyOutputDataModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
 
copyTo(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Copy this DataFile in a other DataFile.
correctSAMRecordForMerging(SAMRecord, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
Changes the given SAMRecord as appropriate for being placed in a file whose header is getSAMHeaderMerger(conf).getMergedHeader().
count(ExpressionCounter, DataFile, ReporterIncrementer, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterUtils
Count the the features.
countDataFormat(DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
 
countDataFormat(DataFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports
Count the number of occurrences of a format in the port.
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
 
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule
 
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule
Group for hadoop counters.
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
 
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
 
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
 
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
 
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
 
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
 
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
 
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
 
COUNTER_GROUP_KEY - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
 
COUNTER_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
 
counterName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
Get the name of the counter.
counterName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
Get the name of the counter.
Counters - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
This class define the counters names used in this package.
Counters() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters
 
CounterSequenceFile - Interface in fr.ens.biologie.genomique.eoulsan.modules.fastqc
This interface extends SequenceFile to add a getCount() method that allow to get the count of the read entries.
CountSplicedReadsModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc
This step computes how many spliced alignments there are in a SAM file.
CountSplicedReadsModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule
 
cpuInfo() - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with CPU informations.
create() - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Create the ports.
create() - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder
Create the ports.
create() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Create an OutputStream for the DataFile.
create() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
createBZip2InputStream(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.io.ApacheCommonCompressionCodecs
Create a bzip2 input stream.
createBZip2InputStream(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.io.HadoopCompressionCodecs
Create a bzip2 input stream.
createBZip2OutputStream(OutputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.io.ApacheCommonCompressionCodecs
Create a bzip2 output stream.
createBZip2OutputStream(OutputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.io.HadoopCompressionCodecs
Create a bzip2 output stream.
createCommand(File, boolean, String, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
Create R command.
createCommandLine(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter
 
createCommandLine(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter
 
createCommandLine(String) - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.ExecutorInterpreter
Create the command line for the the argument of the interpreter.
createCommandLine(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.GenericExecutorInterpreter
 
createConfiguration() - Static method in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
Create a new Configuration object from Eoulsan runtime settings.
createConfiguration(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
Create a new Configuration object from settings.
CREATED - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
 
CreateDesignAction - Class in fr.ens.biologie.genomique.eoulsan.actions
This class define an action to create design file.
CreateDesignAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
 
createEmptyDesign() - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignFactory
Create a design without targets.
createEoulsanDataDirectoryIfRequired() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
Create an "eoulsan-data" directory if mapper indexes or genome description storage has not been defined.
createFileInTempDir(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
Create a file in the temporary directory.
createGenomeDescription(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionCreator
Create genome description object from the storage if already exists or compute it from the genome.
createGenomeDescriptionFromAnnotation(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionCreator
Create genome description object from the storage if already exists or compute it from the genome.
CreateHadoopJarAction - Class in fr.ens.biologie.genomique.eoulsan.actions
This class define an action to create hadoop jar file.
CreateHadoopJarAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
 
createIndex(DataFile, GenomeDescription, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeMapperIndexer
Create an archived genome index.
createInputStream(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Create an input stream from a path.
createLogFileAndFlushLog(URI) - Method in class fr.ens.biologie.genomique.eoulsan.Main
Create a new log file and flush log.
createLogFiles(URI, URI) - Method in class fr.ens.biologie.genomique.eoulsan.Main
Create the log file for Eoulsan and additional log file for dependencies that use their own logging system.
createOtherLog(URI) - Method in class fr.ens.biologie.genomique.eoulsan.Main
Create the additional log file for dependencies that use their own logging system.
createOutputStream(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Create an output stream from a path.
createRecordReader(InputSplit, TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqInputFormat
 
createRecordReader(InputSplit, TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMInputFormat
 
createSAMSequenceDictionaryFromSAMHeader(List<String>) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils
Create a SAMSequenceDictionary from the SAM header in a list of String.
createShutdownHookThread() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
Create a shutdown hook thread.
createSimpleProcess() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor
 
createSimpleProcess() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
Create the process that will execute the R Script.
createStepResult(TaskContextImpl, Throwable) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner
Create a step result for an exception.
createStepResult(TaskContextImpl, Throwable, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner
Create a step result for an exception.
createTaskResult() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus
Create a TaskResult object for a successful result.
createTaskResult() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
createTaskResult(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus
Create a TaskResult object.
createTaskResult(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
createTaskResult(Throwable) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus
Create a TaskResult object.
createTaskResult(Throwable) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
createTaskResult(Throwable, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus
Create a TaskResult object.
createTaskResult(Throwable, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
createTempDir() - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
Create a new temporary directory.
createTempDir(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
Create a new temporary directory.
createTempFile(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
Create a new temporary file.
createTempPath(Path, String, String, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Create a new temporary path.
CUTADAPT_ADAPTER_FASTA - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Cutadapt adapters format.

D

Data - Interface in fr.ens.biologie.genomique.eoulsan.data
This interface define data used by ports.
DATA_FORMAT_PATH_KEY - Static variable in class fr.ens.biologie.genomique.eoulsan.Settings
 
dataEquals(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Test if two files are related to the same data.
dataEquals(File, File) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Test if two files are related to the same data.
dataEquals(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Test if two filenames are related to the same data.
DataFile - Class in fr.ens.biologie.genomique.eoulsan.data
This class define a DataFile.
DataFile(DataFile, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile
Public constructor.
DataFile(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile
Public constructor.
DataFile(File, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile
Public constructor.
DataFile(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile
Public constructor.
DataFile(URI) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile
Public constructor.
DataFile(Path) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile
Public constructor.
DataFile(Path, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile
Public constructor.
dataFileCount(StepOutputPort, Sample, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
Get the count of files that exists for a step, a format and sample (case of multi-files data).
DataFileDataPath - Class in fr.ens.biologie.genomique.eoulsan.data.storages
This class define a bridge between Kenetre DataPath objects and Eoulsan DataFile objects.
DataFileDataPath(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
Constructor.
DataFileDataPath(DataPath, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
Constructor.
DataFileDataPath(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
Constructor.
DataFileDistCp - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload
This class allow to copy and transform data in a distributed manner.
DataFileDistCp(Configuration, Path) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DataFileDistCp
Public constructor.
DataFileDistCp.DistCpMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload
This inner class define the mapper class for DataSourceDistCp map-reduce job.
DataFileGenomeDescStorage - Class in fr.ens.biologie.genomique.eoulsan.data.storages
This class define a storage for genome description files using DataFile API.
DataFileGenomeDescStorage(DataPath, GenericLogger) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeDescStorage
Protected constructor.
DataFileGenomeIndexStorage - Class in fr.ens.biologie.genomique.eoulsan.data.storages
This class define a storage for genome indexes using DataFile API.
DataFileGenomeIndexStorage(DataPath, GenericLogger) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage
Constructor.
DataFileGenomeMapperIndexer - Class in fr.ens.biologie.genomique.eoulsan.data.storages
This class define a genome mapper indexer.
DataFileGenomeMapperIndexer(MapperInstance, String, Map<String, String>, int, GenomeIndexStorage, File, GenericLogger) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeMapperIndexer
Public constructor.
DataFileMetadata - Interface in fr.ens.biologie.genomique.eoulsan.data
This class define source metadata
DataFiles - Class in fr.ens.biologie.genomique.eoulsan.data
This class contains utility methods on DataFile objects.
DataFiles() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFiles
 
DataFileStorage - Class in fr.ens.biologie.genomique.eoulsan.data.storages
This class define a storage using DataFile API.
DataFileStorage(String, List<String>) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileStorage
Constructor.
DataFormat - Interface in fr.ens.biologie.genomique.eoulsan.data
This interface define a DataFormat.
DataFormatConverter - Class in fr.ens.biologie.genomique.eoulsan.data
This class allow to copy and transform data while copying.
DataFormatConverter(DataFile, DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFormatConverter
Constructor
DataFormatConverter(DataFile, DataFile, DataFormat, OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFormatConverter
Constructor
DataFormatConverter(DataFile, DataFile, OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFormatConverter
Constructor
DataFormatRegistry - Class in fr.ens.biologie.genomique.eoulsan.data
this class register DataFormat to allow get the DataFormat of a file from its filename.
DataFormats - Class in fr.ens.biologie.genomique.eoulsan.data
This class contains the definition of some DataFormats.
DataFormats() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFormats
 
DATAFORMATS_TO_DOWNLOAD_SETTING - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
Key in the settings to use to save the list of DataFormat of the files to download.
DataList - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a data list.
DataMetadata - Interface in fr.ens.biologie.genomique.eoulsan.data
This interface define metadata of data objects.
DataMetadataStorage - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a storage for data metadata of all files generated by the workflow.
DataProtocol - Interface in fr.ens.biologie.genomique.eoulsan.data.protocols
This interface define a protocol.
DataProtocolService - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define a service to retrieve a DataProtocol.
DataToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements
The Class ToolOutputsData.
DataToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement
Instantiates a new tool outputs data.
DataUtils - Class in fr.ens.biologie.genomique.eoulsan.core
This class define an utility on data object.
DATE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
 
deadEvent(DeadEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowEventBus
 
DEBUG - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Set the debug mode.
decompressInputStreamIsNeeded(InputStream, String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
Decompress an inputStream if needed.
DeepToolsModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling
This class uses tools from the DeepTools suite.
DeepToolsModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
 
DEFAULT_CHARSET - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Default charset.
DEFAULT_FILE_ENCODING - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Default file encoding.
DEFAULT_LOCALE - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Default locale of the application.
DEFAULT_R_LANG - Static variable in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
 
DEFAULT_SINGLE_INPUT_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Default single input port name.
DEFAULT_SINGLE_OUTPUT_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder
Default single output port name.
DefaultDesignReader - Class in fr.ens.biologie.genomique.eoulsan.design.io
This class allow to read a design file whatever the underlying design format.
DefaultDesignReader(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DefaultDesignReader
Public constructor.
DefaultDesignReader(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DefaultDesignReader
Public constructor.
DefaultDesignReader(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DefaultDesignReader
Public constructor
DefaultDesignReader(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DefaultDesignReader
Public constructor
DefaultExecutorInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters
This class define the default executor interpreter.
DefaultExecutorInterpreter() - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter
 
DefineDataFormatToDownload - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload
This Step allow to define the list of the formats of the files to download at the end of a Hadoop execution.
DefineDataFormatToDownload() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
 
defineSampleSubDirName(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder
Get the sample sub directory.
delete() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Delete the DataFile.
delete(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Delete the DataFile.
delete(DataFile, boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Delete a file.
delete(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
delete(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
 
deleteOnExit(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
 
deleteOnExit(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow
Delete a file on the exit of the workflow.
DeprecatedDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define a deprecated protocol.
DeprecatedDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
Constructor.
DeprecatedDataProtocol(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
Constructor.
deprecatedParameter(StepConfigurationContext, Parameter) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Show a message for deprecated parameters.
deprecatedParameter(StepConfigurationContext, Parameter, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Show a message for deprecated parameters.
deprecatedParameter(String, Parameter, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Show a message for deprecated parameters.
description() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
 
DESCRIPTION_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
 
DESeq2 - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana
This class contains methods to run the differential analysis module DESeq2.
DESeq2(RExecutor, String, Design, Experiment, Map<String, File>, boolean, boolean, boolean, boolean, DESeq2.SizeFactorsType, DESeq2.FitType, DESeq2.StatisticTest, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2
Public constructor.
DESeq2.FitType - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana
Enum for the fitType option in DESeq2 related to the dispersion estimation.
DESeq2.SizeFactorsType - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana
Enum for the sizeFactorsType option in DESeq2 related to the estimation of the size factor.
DESeq2.StatisticTest - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana
Enum for the statisticTest option in DESeq2 related to the statistic test to be used during the differential expression analysis
DESeq2DesignChecker - Class in fr.ens.biologie.genomique.eoulsan.checkers
This class define a Checker on the design for DESeq2 analyzes.
DESeq2DesignChecker() - Constructor for class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
 
DESeq2Module - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana
Class to run the differential analysis with DEseq2
DESeq2Module() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
 
deserialize(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Deserialize the TaskContext object.
deserialize(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
Deserialize the TaskResult object.
deserialize(File) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Deserialize the TaskContext object.
deserialize(File) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
Deserialize the TaskResult object.
deserialize(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Deserialize the TaskContext object.
deserialize(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
Deserialize the TaskResult object.
deserializeOutputData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Deserialize output data.
deserializeOutputData(File) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Deserialize output data.
deserializeOutputData(InputStream) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Deserialize output data.
design - Variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
 
Design - Interface in fr.ens.biologie.genomique.eoulsan.design
This interface defines the design.
DESIGN_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
 
DESIGN_FILE_PATH_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Design file path constant name.
DESIGN_FILE_VERSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Design file version.
DESIGN_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
 
DesignBuilder - Class in fr.ens.biologie.genomique.eoulsan.design
This class allow to easily build Design object from files paths.
DesignBuilder() - Constructor for class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder
Public constructor.
DesignBuilder(String[]) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder
Public constructor.
DesignFactory - Class in fr.ens.biologie.genomique.eoulsan.design
This class is a factory for experimental design.
DesignFormatFinderInputStream - Class in fr.ens.biologie.genomique.eoulsan.design.io
This class allow to automatically detect the format of a design file.
DesignFormatFinderInputStream(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DesignFormatFinderInputStream
Public constructor.
DesignMetadata - Interface in fr.ens.biologie.genomique.eoulsan.design
This interface defines the design metadata.
DesignMetadataImpl - Class in fr.ens.biologie.genomique.eoulsan.design
This class defines the default implementation of the design metadata.
DesignModule - Class in fr.ens.biologie.genomique.eoulsan.modules
This class define a design module.
DesignModule(Design, CheckerModule) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
Constructor.
DesignReader - Interface in fr.ens.biologie.genomique.eoulsan.design.io
This interface define a DesignReader.
DesignUtils - Class in fr.ens.biologie.genomique.eoulsan.design
Utils methods for Design.
DesignWriter - Interface in fr.ens.biologie.genomique.eoulsan.design.io
This interface define a writer for designs.
DiffAna - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana
This class create and launch a R script to compute differential analysis.
DiffAna(RExecutor, Design, DiffAna.DispersionMethod, DiffAna.DispersionSharingMode, DiffAna.DispersionFitType) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna
Public constructor.
DIFFANA_RESULTS_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Diffana results data format.
DiffAna.DispersionFitType - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana
Dispersion estimation fitType enum for DESeq differential analysis
DiffAna.DispersionMethod - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana
Dispersion estimation method enum for DESeq differential analysis
DiffAna.DispersionSharingMode - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana
Dispersion estimation sharingMode enum for DESeq differential analysis
DiffAnaModule - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana
This class define the module of differential analysis in local mode.
DiffAnaModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
 
DiffanaResultsAnnotationModule - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana
This class define a module that create annotated expression files in TSV, ODS or XLSX format.
DiffanaResultsAnnotationModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
 
disConnect() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Destroy the connection to the Rserve server.
DISCUSSION_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Project discussion group.
diskFreeInfo(File) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Get information about the partition of a file.
DistCp - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop
A Map-reduce program to recursively copy directories between different file-systems.
DistCp(Configuration) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp
 
DistCp.DuplicationException - Exception in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop
An exception class for duplicated source files.
DistCpMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DataFileDistCp.DistCpMapper
 
DistributedLock - Class in fr.ens.biologie.genomique.eoulsan.util.locker
Distributed locking via ZooKeeper.
DistributedLock(ZooKeeper, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock
 
DistributedLock(ZooKeeper, String, Iterable<ACL>) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock
Creates a distributed lock using the given zkClient to coordinate locking.
DistributedLocker - Class in fr.ens.biologie.genomique.eoulsan.util.locker
This class implements a locker using Zookeeper based on Twiter's DistributedLock class.
DistributedLocker(String, int, String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLocker
Public constructor.
DOCKER - fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory.Mode
 
DOCKER_IMAGE_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration
 
DockerExecutorInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters
This class define a Docker executor interpreter.
DockerExecutorInterpreter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter
Constructor.
dockerInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with Docker configuration informations.
DockerRequirement - Class in fr.ens.biologie.genomique.eoulsan.requirements
This class define a Docker requirement.
DockerRequirement() - Constructor for class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
 
DockerRExecutor - Class in fr.ens.biologie.genomique.eoulsan.util.r
This class define a Docker RExecutor.
DockerRExecutor(File, File, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor
Constructor.
DONE - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
 
DUMMY_TXT - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Dummy format.
DummyGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators
This class implements a dummy generator module that create an empty file.
DummyGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
 
DummyTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This class define a Dummy cluster scheduler.
DummyTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.DummyTaskScheduler
Constructor.

E

elapsed(TimeUnit) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.SerializableStopwatch
 
ELIMINATED_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
EmergencyStopTask - Interface in fr.ens.biologie.genomique.eoulsan.core.workflow
This interface define a task that will executed if the execution of the workflow fail.
EmergencyStopTasks - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a class where the emergency tasks are stored
EMPTY_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
EmptyFileQC - Class in fr.ens.biologie.genomique.eoulsan.modules.fastqc
Empty file FastQC module.
EmptyFileQC(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
Constructor.
EmptyToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements
This class define an empty tool element.
EmptyToolElement() - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
Public constructor.
EmptyToolElement(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
Public constructor.
EmptyToolElement(String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
Public constructor.
encodeAllowedCompressionsParameterValue(EnumSet<CompressionType>) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
Method to encode an EnumSet of the allowed compressions parameter in a string.
endWork(Ticket) - Method in interface fr.ens.biologie.genomique.eoulsan.util.locker.TicketScheduler
Inform the scheduler that the ticket job has been finished.
endWork(Ticket) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.TicketSchedulerServer
 
ENTRIES_READ - Static variable in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters
 
ENTRIES_WRITTEN - Static variable in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters
 
entrySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
entrySet() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
Get an entry set of the metadata.
entrySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
entrySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
EOULSAN_CLASSPATH_JVM_ARG - Static variable in class fr.ens.biologie.genomique.eoulsan.Main
 
EOULSAN_MEMORY - Static variable in class fr.ens.biologie.genomique.eoulsan.Main
 
EOULSAN_PATH - Static variable in class fr.ens.biologie.genomique.eoulsan.Main
 
EOULSAN_SCRIPT - Static variable in class fr.ens.biologie.genomique.eoulsan.Main
 
EOULSAN_TOOLS_WEBSITE_URL - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Eoulsan tools website URL.
Eoulsan1DesignReader - Class in fr.ens.biologie.genomique.eoulsan.design.io
This class define a design reader for limma design files.
Eoulsan1DesignReader(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignReader
Public constructor.
Eoulsan1DesignReader(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignReader
Public constructor.
Eoulsan1DesignReader(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignReader
Public constructor.
Eoulsan1DesignReader(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignReader
Public constructor.
Eoulsan1DesignWriter - Class in fr.ens.biologie.genomique.eoulsan.design.io
This class implements a writer for limma design files.
Eoulsan1DesignWriter(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter
Public constructor.
Eoulsan1DesignWriter(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter
Public constructor.
Eoulsan1DesignWriter(OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter
Public constructor.
Eoulsan1DesignWriter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter
Public constructor.
Eoulsan2DesignReader - Class in fr.ens.biologie.genomique.eoulsan.design.io
This class define a design reader for Eoulsan 2 design file.
Eoulsan2DesignReader(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignReader
Public constructor.
Eoulsan2DesignReader(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignReader
Public constructor.
Eoulsan2DesignReader(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignReader
Public constructor.
Eoulsan2DesignReader(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignReader
Public constructor.
Eoulsan2DesignWriter - Class in fr.ens.biologie.genomique.eoulsan.design.io
This class implements a writer for Eoulsan 2 design files.
Eoulsan2DesignWriter(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter
Public constructor.
Eoulsan2DesignWriter(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter
Public constructor.
Eoulsan2DesignWriter(OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter
Public constructor.
Eoulsan2DesignWriter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter
Public constructor.
EoulsanAnnotationUtils - Class in fr.ens.biologie.genomique.eoulsan.annotations
This class contains annotation utilities.
EoulsanDockerManager - Class in fr.ens.biologie.genomique.eoulsan.util
This class define a Docker manager configurated with Eoulsan settings.
EoulsanError - Error in fr.ens.biologie.genomique.eoulsan
A nestable Eoulsan error.
EoulsanError() - Constructor for error fr.ens.biologie.genomique.eoulsan.EoulsanError
Create a new EoulsanError.
EoulsanError(String) - Constructor for error fr.ens.biologie.genomique.eoulsan.EoulsanError
Create a new EoulsanError with a message.
EoulsanException - Exception in fr.ens.biologie.genomique.eoulsan
A nestable Eoulsan exception.
EoulsanException() - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanException
Create a new EoulsanException.
EoulsanException(String) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanException
Create a new EoulsanException with a message.
EoulsanException(String, Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanException
Create a new EoulsanException with a message and a cause.
EoulsanException(Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanException
Create a new EoulsanException with a cause.
EoulsanITRuntimeException - Exception in fr.ens.biologie.genomique.eoulsan
This class define a runtime exception for integration tests.
EoulsanITRuntimeException() - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException
Create a new EoulsanITRuntimeException.
EoulsanITRuntimeException(String) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException
Create a new EoulsanITRuntimeException with a message.
EoulsanITRuntimeException(String, Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException
Create a new EoulsanITRuntimeException with a message and a cause.
EoulsanITRuntimeException(Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException
Create a new EoulsanITRuntimeException with a cause.
EoulsanLogger - Class in fr.ens.biologie.genomique.eoulsan
This class allow to change the logger name for all Eoulsan classes.
EoulsanLogger() - Constructor for class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
 
EoulsanRuntime - Class in fr.ens.biologie.genomique.eoulsan
This class store the only Eoulsan runtime instance.
EoulsanRuntimeException - Exception in fr.ens.biologie.genomique.eoulsan
A nestable Eoulsan exception.
EoulsanRuntimeException() - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException
Create a new EoulsanRuntimeException.
EoulsanRuntimeException(String) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException
Create a new EoulsanRuntimeException with a message.
EoulsanRuntimeException(String, Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException
Create a new EoulsanException with a message and a cause.
EoulsanRuntimeException(Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException
Create a new EoulsanException with a cause.
EoulsanTranslatorUtils - Class in fr.ens.biologie.genomique.eoulsan.util
This class define Kenetre translator utility glue methods for Eoulsan.
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl
 
equals(Object) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.Infos.Info
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJobEmergencyStopTask
 
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
ERROR_CODE - Static variable in exception fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp.DuplicationException
Error code for this exception
errorExit(Throwable, String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
Print error message to the user and exits the application.
errorExit(Throwable, String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
Print error message to the user and exits the application.
errorHalt(Throwable, String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
Print error message to the user and halts the application.
errorHalt(Throwable, String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
Print error message to the user and halts the application.
escapeUnderScore(String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Escape underscore for LaTeX title.
exceptionMessage - Variable in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessThreadErrOutput
 
exec(String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
Execute a command with the OS.
ExecAction - Class in fr.ens.biologie.genomique.eoulsan.actions
This class define the Local exec Action.
ExecAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ExecAction
 
ExecFileLock - Class in fr.ens.biologie.genomique.eoulsan.util.locker
This class define a lock file.
ExecFileLock(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.ExecFileLock
Public constructor.
ExecJarHadoopAction - Class in fr.ens.biologie.genomique.eoulsan.actions
This class define an action that allow to execute a jar on an Hadoop cluster.
ExecJarHadoopAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
 
ExecLock - Class in fr.ens.biologie.genomique.eoulsan.util.locker
This class define a lock to prevent execution of a process simultaneously on multiples JVM.
ExecLock(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.ExecLock
Public constructor.
ExecLock(String, File) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.ExecLock
Public constructor.
execThreadOutput(String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
Execute a command and write the content of the standard output and error to System.out and System.err.
execThreadOutput(String[]) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
Execute a command and write the content of the standard output and error to System.out and System.err.
execToString(String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
Execute a command with the OS and return the output in a string.
execToString(String, boolean, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
Execute a command with the OS and return the output in a string.
execute() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
Execute the workflow.
execute() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.Executor
run Eoulsan.
execute() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter
Execute script by Python interpreter and replace variable name by value.
execute(TaskContext) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter
Convert command tag from tool file in string, variable are replace by value.
execute(TaskContext, TaskStatus) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module
Execute a task step.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule
Merge input replicates.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
Run bedtools multiinter.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
Run deeptools.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
Run macs2.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule
Install all the files necessary in the tmp folder, then run idr.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule
Install all the files necessary in the tmp folder, then run idr.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
Run trackhub generator.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.local.ExpressionLocalModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FirstModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.FilterAndMapReadsHadoopModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterHadoopModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperHadoopModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAM2BAMHadoopModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterHadoopModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.BAM2SAMLocalModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsFilterLocalModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAM2BAMLocalModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAM2FASTQLocalModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAMFilterLocalModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.Splice2BEDModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
 
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.TerminalModule
 
execute(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskSerializationUtils
Execute a task context serialization file.
execute(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskSerializationUtils
Execute a task context serialization file.
execute(List<Module>, List<Module>) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.Executor
run Eoulsan.
execute(List<String>, File, File, File, File, File...) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.AbstractExecutorInterpreter
 
execute(List<String>, File, File, File, File, File...) - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.ExecutorInterpreter
Execute a command line.
executeRCode(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Execute a R code.
executeRnwCode(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Execute a R Sweave code.
executeRnwCode(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Execute a R Sweave code.
executeRScript(File, boolean, String, File, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
Execute a R script.
executeRScript(File, boolean, String, File, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
 
executeRScript(File, boolean, String, File, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
 
executeRScript(String, boolean, String, boolean, String, DataFile, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
 
executeRScript(String, boolean, String, boolean, String, DataFile, String...) - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor
Execute a R script.
executeTask(TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
Default executing context method.
EXECUTION_MODE_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration
 
ExecutionMode - Enum in fr.ens.biologie.genomique.eoulsan.annotations
This class define an enum for the execution mode of Eoulsan.
executor - Variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
 
Executor - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class is the executor for running all the steps of an analysis.
Executor(ExecutorArguments) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.Executor
Constructor.
ExecutorArguments - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class contains arguments for the Executor.
ExecutorArguments() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Public constructor.
ExecutorArguments(long) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Public constructor.
ExecutorArguments(File, File) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Public constructor.
ExecutorInterpreter - Interface in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters
This interface define a executor interpreter for Galaxy tools.
execWriteOutput(String, File) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
Execute a command with the OS and save the output in file.
exists() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Check if this DataFile exists.
exists() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
exists(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Check if this DataFile exists.
exists(DataFile, boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Test a source exists.
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
 
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
 
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
 
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
 
exists(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Test if a path exists
exit(int) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
Exit the application.
Experiment - Interface in fr.ens.biologie.genomique.eoulsan.design
This interface defines an experiment.
ExperimentImpl - Class in fr.ens.biologie.genomique.eoulsan.design
This class defines the default implementation of an experiment.
ExperimentMetadata - Interface in fr.ens.biologie.genomique.eoulsan.design
This interface defines the experiment metadata.
ExperimentSample - Interface in fr.ens.biologie.genomique.eoulsan.design
This interface defines the experiment sample.
ExperimentSampleImpl - Class in fr.ens.biologie.genomique.eoulsan.design
This class defines the default implementation of the experiment sample.
ExperimentSampleMetadata - Interface in fr.ens.biologie.genomique.eoulsan.design
This inteface defines the experiment sample metadata.
ExperimentSampleMetadataImpl - Class in fr.ens.biologie.genomique.eoulsan.design
This class defines the default implementation of the experiment sample metadata.
EXPRESSION_MATRIX_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Expression matrix.
EXPRESSION_RESULTS_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Expression results data format.
ExpressionCounterCounter - Enum in fr.ens.biologie.genomique.eoulsan.modules.expression
This enum define counters for the expression step.
ExpressionCounterUtils - Class in fr.ens.biologie.genomique.eoulsan.modules.expression
This class define some glue methods between Eoulsan and Kenetre.
expressionFilesPrefix - Variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
 
expressionFilesSuffix - Variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
 
ExpressionHadoopModule - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop
This class is the main class for the expression program of the reads in hadoop mode.
ExpressionHadoopModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule
 
ExpressionInputPreprocessor - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc
This class define a preprocessor for expression reports.
ExpressionInputPreprocessor() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor
 
ExpressionLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.local
This class is the module to compute expression in local mode
ExpressionLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.local.ExpressionLocalModule
 
ExpressionMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop
Mapper for the expression estimation.
ExpressionMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionMapper
 
ExpressionMerger - Class in fr.ens.biologie.genomique.eoulsan.splitermergers
This class define a merger class for expression files.
ExpressionMerger() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionMerger
 
ExpressionOutputFormat - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
This class define a expression output format.
ExpressionOutputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.ExpressionOutputFormat
 
ExpressionRecordWriter - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
This class define a RecordWriter for expression files.
ExpressionRecordWriter(TaskAttemptContext, DataOutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.ExpressionRecordWriter
Public constructor.
ExpressionReducer - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop
Reducer for the expression estimation.
ExpressionReducer() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionReducer
 
ExpressionResultsAnnotationModule - Class in fr.ens.biologie.genomique.eoulsan.modules.expression
This class define a module that create annotated expression files in TSV, ODS or XLSX format.
ExpressionResultsAnnotationModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
 
ExpressionSAMOutputMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop
Mapper for the expression estimation with a SAM output.
ExpressionSAMOutputMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionSAMOutputMapper
 
ExpressionSplitter - Class in fr.ens.biologie.genomique.eoulsan.splitermergers
This class define a splitter class for expression files.
ExpressionSplitter() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionSplitter
 
ExpressionToMatrixModule - Class in fr.ens.biologie.genomique.eoulsan.modules.singlecell
This class define a class that allow to merge expression file into a matrix file.
ExpressionToMatrixModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
 
EXTERNAL_APP - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
 
extractCheetahScript(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract command tag in string.
extractChildElementsByTagName(Element, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract child elements by tag name.
extractConditionalParamElement(ToolInfo, Element) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract conditional param element.
extractConditionalParamElement(ToolInfo, Element, Map<String, Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract conditional param element.
extractDescription(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract description tag in string.
extractDockerImage(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract docker image attribute in string.
extractElementsByTagName(ToolInfo, Document, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract elements by tag name.
extractElementsByTagName(ToolInfo, Document, String, int) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract elements by tag name.
extractElementsByTagName(Element, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract elements by tag name.
extractElementsByTagName(Element, String, int) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract elements by tag name.
extractInputs(ToolInfo, Document, Map<String, Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract all input parameters define in document.
extractInterpreters(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract interpreter attribute in string.
extractOutputs(ToolInfo, Document, Map<String, Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract all output parameters define in document.
extractParamElement(ToolInfo, Element, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract parameter elements.
extractParamElement(ToolInfo, Element, String, Map<String, Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract parameter elements.
extractToolID(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract tool id tag in string.
extractToolName(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract tool name tag in string.
extractToolVersion(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract tool version attribute in string.
extractValueFromElement(Document, String, int, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Extract text from DOM from tag name, at the index place.

F

FAILED - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
 
FailModule - Class in fr.ens.biologie.genomique.eoulsan.modules
This module is a module that always fails.
FailModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.FailModule
 
FakeModule - Class in fr.ens.biologie.genomique.eoulsan.modules
This module is a fake module.
FakeModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
 
FASTA_FILE_WIDTH - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
FASTA file width.
FASTQ_FORMAT_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
 
FASTQ_FORMAT_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
 
FASTQC_CASAVA_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
Format fastq type casava/Illumina
FASTQC_EXPGROUP_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
Use exponential base groups in graph
FASTQC_KMER_SIZE_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
Collector FastQC kmer size
FASTQC_NOFILTER_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
Option for filter fastq file if casava=true for all modules
FASTQC_NOGROUP_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
Collector FastQC nogroup
FASTQC_REPORT_HTML - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
FastQC HTML report format.
FASTQC_REPORT_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
FastQC ZIP report format.
FastQCInputPreprocessor - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc
This class define a preprocessor for FastQC reports.
FastQCInputPreprocessor() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor
 
FastQCModule - Class in fr.ens.biologie.genomique.eoulsan.modules.fastqc
This class define a module that compute QC report using FastQC.
FastQCModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
 
FastQCRuntimePatcher - Class in fr.ens.biologie.genomique.eoulsan.modules.fastqc
This class to patch FastQC to be compatible with Hadoop.
FastQCRuntimePatcher() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCRuntimePatcher
 
FastqInputFormat - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
This class define an InputFormat for FASTQ files for the Hadoop MapReduce framework.
FastqInputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqInputFormat
 
FastqLineRecordReader - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
Treats keys as offset in file and value as line.
FastqLineRecordReader() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
 
FastqLineRecordReader(byte[]) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
 
FastqMerger - Class in fr.ens.biologie.genomique.eoulsan.splitermergers
This class define a merger class for FASTQ files.
FastqMerger() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqMerger
 
FastqOutputFormat - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
This class define a FASTQ output format.
FastqOutputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqOutputFormat
 
FastqPairedEndReducer() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PairedEndFastqToTfq.FastqPairedEndReducer
 
FastqRecordReader - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
This class define a RecordReader for FASTQ files for the Hadoop MapReduce framework.
FastqRecordReader(TaskAttemptContext) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
Public constructor.
FastqRecordWriter - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
This class define a RecordWriter for FASTQ files.
FastqRecordWriter(TaskAttemptContext, DataOutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordWriter
Public constructor.
FastqSequenceFile - Class in fr.ens.biologie.genomique.eoulsan.modules.fastqc
This class define a SequenceFile for FASTQ files.
FastqSequenceFile(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
Public constructor.
FastqSplitter - Class in fr.ens.biologie.genomique.eoulsan.splitermergers
This class define a splitter class for FASTQ files.
FastqSplitter() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqSplitter
 
FEATURECOUNTS_SUMMARY_TXT - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
FeatureCounts summary format.
FeatureCountsInputPreprocessor - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc
This class define a preprocessor for FeatureCounts reports.
FeatureCountsInputPreprocessor() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor
 
FEATURES_FILE_FORMAT_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
 
file(StepOutputPort, DataElement, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming
Create a DataFile object for a file of the workflow.
FileCharsets - Class in fr.ens.biologie.genomique.eoulsan.io
This class define default charsets.
FileConcatInputStream - Class in fr.ens.biologie.genomique.eoulsan.io
This class define an InputStream that concatenate files in an InputStream.
FileConcatInputStream(List<File>) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.FileConcatInputStream
Constructor.
FileDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class implements a File Protocol.
FileDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
fileMiddle() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Return the middle string of the filename.
fileMiddle(StepOutputPort, DataElement, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming
Create the middle of a filename.
fileMiddle(StepOutputPort, String, int, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming
Create the middle of a filename.
fileMiddle(String, int, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Create the middle of a filename.
filename() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Return the filename.
filename(StepOutputPort, DataElement, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming
Create the name of a data file of the workflow.
filename(String, String, DataFormat, String, int, int, CompressionType) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Create the filename from several parameters.
FileNaming - Class in fr.ens.biologie.genomique.eoulsan.core
This class contains methods to create workflow data file names.
FileNaming() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Private constructor.
FileNamingParsingRuntimeException - Exception in fr.ens.biologie.genomique.eoulsan.core
This class define a runtime exception for filename parsing errors.
FileNamingParsingRuntimeException() - Constructor for exception fr.ens.biologie.genomique.eoulsan.core.FileNamingParsingRuntimeException
Create a new FileNamingParsingRuntimeException.
FileNamingParsingRuntimeException(String) - Constructor for exception fr.ens.biologie.genomique.eoulsan.core.FileNamingParsingRuntimeException
Create a new FileNamingParsingRuntimeException with a message.
filePrefix() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Return the file prefix.
filePrefix(StepOutputPort) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming
Create the prefix of a filename.
filePrefix(String, String, DataFormat) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Create the prefix of a filename.
filePrefix(String, String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Create the prefix of a filename.
FileResourceLoader<S> - Class in fr.ens.biologie.genomique.eoulsan.util
This class allow to define a resource loader for files.
FileResourceLoader(Class<S>, DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader
Public constructor.
fileSuffix() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Return the file suffix.
fileSuffix(StepOutputPort) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming
Create the suffix of a filename.
fileSuffix(DataFormat, CompressionType) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Create the suffix of a file.
fileSuffix(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Create the suffix of a file.
fillBuffer(InputStream, byte[], boolean) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.CompressedSplitFastqLineReader
 
FilterAndMapReadsHadoopModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class define a Step that filter and map read in Hadoop mode.
FilterAndMapReadsHadoopModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.FilterAndMapReadsHadoopModule
 
FinalExpressionFeaturesCreator - Class in fr.ens.biologie.genomique.eoulsan.modules.expression
This class generates the final expression file after counting the alignments for each feature with HTSeq-count.
FinalExpressionFeaturesCreator(ExpressionCounter) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.FinalExpressionFeaturesCreator
Public constructor.
FIRST_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
 
FirstModule - Class in fr.ens.biologie.genomique.eoulsan.modules
This class define a first module that do nothing.
FirstModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.FirstModule
 
FIT_ONLY - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode
 
FloatParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements
This class define a float tool element parameter.
FloatParameterToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement
Instantiates a new float tool parameter.
FloatParameterToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement
Instantiates a new float tool parameter.
flush() - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler
 
flush() - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterOutputStream
 
flushLog() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Flush log.
FORMAT_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
 
FORMATS_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
 
FormatsAction - Class in fr.ens.biologie.genomique.eoulsan.actions
This class define an action that show the list of available formats.
FormatsAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.FormatsAction
 
fr.ens.biologie.genomique.eoulsan - package fr.ens.biologie.genomique.eoulsan
Root package of Eoulsan.
fr.ens.biologie.genomique.eoulsan.actions - package fr.ens.biologie.genomique.eoulsan.actions
This package contains all the commands (actions) available through the Eoulsan command line.
fr.ens.biologie.genomique.eoulsan.annotations - package fr.ens.biologie.genomique.eoulsan.annotations
This package define the annotations on Eoulsan classes plug-ins.
fr.ens.biologie.genomique.eoulsan.bio.io.hadoop - package fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
This package contains I/O classes for reading objects of the fr.ens.biologie.genomique.eoulsan.bio.alignmentsfilters package from Hadoop.
fr.ens.biologie.genomique.eoulsan.checkers - package fr.ens.biologie.genomique.eoulsan.checkers
This package contains and define checkers of DataFormat.
fr.ens.biologie.genomique.eoulsan.core - package fr.ens.biologie.genomique.eoulsan.core
This package contains Eoulsan workflow core class.
fr.ens.biologie.genomique.eoulsan.core.schedulers - package fr.ens.biologie.genomique.eoulsan.core.schedulers
This package contains classes for schedulers.
fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters - package fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This package contains classes for cluster schedulers.
fr.ens.biologie.genomique.eoulsan.core.workflow - package fr.ens.biologie.genomique.eoulsan.core.workflow
This package contains Eoulsan workflow dedicated classes.
fr.ens.biologie.genomique.eoulsan.data - package fr.ens.biologie.genomique.eoulsan.data
This package contains classes for data files, data types and data formats.
fr.ens.biologie.genomique.eoulsan.data.protocols - package fr.ens.biologie.genomique.eoulsan.data.protocols
This package contains class for protocols used by the DataFile classes.
fr.ens.biologie.genomique.eoulsan.data.storages - package fr.ens.biologie.genomique.eoulsan.data.storages
This package contains and define data storages.
fr.ens.biologie.genomique.eoulsan.design - package fr.ens.biologie.genomique.eoulsan.design
This package contains classes to handle experimental designs.
fr.ens.biologie.genomique.eoulsan.design.io - package fr.ens.biologie.genomique.eoulsan.design.io
This package contains I/O classes to read and write design files.
fr.ens.biologie.genomique.eoulsan.galaxytools - package 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 - package 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.galaxytools.executorinterpreters - package fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters
This package contain classes related to the Galaxy tool executor interpreters.
fr.ens.biologie.genomique.eoulsan.io - package fr.ens.biologie.genomique.eoulsan.io
This package contains general I/O classes for Eoulsan (not dedicated to fr.ens.biologie.genomique.eoulsan.bio package).
fr.ens.biologie.genomique.eoulsan.modules - package fr.ens.biologie.genomique.eoulsan.modules
This package define the steps for the Eoulsan workflow.
fr.ens.biologie.genomique.eoulsan.modules.chipseq - package fr.ens.biologie.genomique.eoulsan.modules.chipseq
This packages contains the ChIP-Seq modules.
fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling - package fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling
This packages contains the peak-calling modules.
fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc - package 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 - package 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 - package 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 - package 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.expression.local - package fr.ens.biologie.genomique.eoulsan.modules.expression.local
This package contain all the classes related to the expression step in local mode.
fr.ens.biologie.genomique.eoulsan.modules.fastqc - package fr.ens.biologie.genomique.eoulsan.modules.fastqc
This package contain all the classes related to FastQC.
fr.ens.biologie.genomique.eoulsan.modules.generators - package fr.ens.biologie.genomique.eoulsan.modules.generators
This package contain generator steps.
fr.ens.biologie.genomique.eoulsan.modules.mapping - package 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 - package 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.mapping.hadoop.hadoopbamcli - package fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli
 
fr.ens.biologie.genomique.eoulsan.modules.mapping.local - package fr.ens.biologie.genomique.eoulsan.modules.mapping.local
This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in local mode.
fr.ens.biologie.genomique.eoulsan.modules.mgmt - package fr.ens.biologie.genomique.eoulsan.modules.mgmt
This package contain classes related data management (e.g.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop - package 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 - package 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 - package fr.ens.biologie.genomique.eoulsan.modules.multiqc
 
fr.ens.biologie.genomique.eoulsan.modules.singlecell - package fr.ens.biologie.genomique.eoulsan.modules.singlecell
 
fr.ens.biologie.genomique.eoulsan.requirements - package fr.ens.biologie.genomique.eoulsan.requirements
This package contains requirement classes for Eoulsan.
fr.ens.biologie.genomique.eoulsan.splitermergers - package 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.ui - package fr.ens.biologie.genomique.eoulsan.ui
This package contains Eoulsan user interface classes.
fr.ens.biologie.genomique.eoulsan.util - package fr.ens.biologie.genomique.eoulsan.util
This package contain utility classes.
fr.ens.biologie.genomique.eoulsan.util.hadoop - package fr.ens.biologie.genomique.eoulsan.util.hadoop
This package contains utility classes for hadoopS.
fr.ens.biologie.genomique.eoulsan.util.locker - package fr.ens.biologie.genomique.eoulsan.util.locker
This package contain an advanced multi JVM lock system.
fr.ens.biologie.genomique.eoulsan.util.r - package fr.ens.biologie.genomique.eoulsan.util.r
This package contain utility classes for R usage.
FTPPathDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define the FTP protocol in Hadoop mode.
FTPPathDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPPathDataProtocol
 
FTPURLDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define the ftp protocol in local mode.
FTPURLDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPURLDataProtocol
 
fullyDelete(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Fully delete a file of the content of a directory

G

GALAXY_TOOL_PATH_KEY - Static variable in class fr.ens.biologie.genomique.eoulsan.Settings
 
GalaxyToolInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools
This class create an interpreter to tool xml file from Galaxy.
GalaxyToolInterpreter(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter
Public constructor.
GalaxyToolInterpreter(InputStream, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter
Public constructor.
GalaxyToolModule - Class in fr.ens.biologie.genomique.eoulsan.modules
The Class GalaxyToolStep.
GalaxyToolModule(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
Constructor.
GalaxyToolModule(InputStream, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
Constructor.
GalaxyToolXMLParserUtils - Class in fr.ens.biologie.genomique.eoulsan.galaxytools
This class define static utils methods to extract data in Galaxy tool XML file.
GalaxyToolXMLParserUtils() - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
 
GAPPED_PEAK - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.ChIPSeqDataFormats
Gapped peak format.
GENE_EST_ONLY - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode
 
generalConf(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with general configuration informations.
generateConditionPart(List<String>, StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Add condition vector to R script.
generateExpressionFileNamesPart(StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Add expression file name vector to R script.
generateRepTechGroupPart(List<String>, StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Write the section of the script that handle technical replicate groups.
generateRnwpreamble(List<Sample>, String, String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Write Rnw preamble.
generateSampleIdsPart(List<Integer>, StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Add SampleIds vector to R script.
generateSampleNamePart(List<String>, StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Add sampleNames vector to R script.
generateScript(Experiment, TaskContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna
 
generateScript(Experiment, TaskContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Generate the R script.
Generator - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations
This annotation is used to mark a step class that is a generator with user custom parameters.
GENERATOR_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
 
GenericExecutorInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters
This class define a generic executor interpreter.
GenericExecutorInterpreter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.GenericExecutorInterpreter
Constructor.
GenericStorageGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators
This module allow to easily store output of generator to avoid computation at each Eoulsan startup.
GenericStorageGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
 
GENOME_DESC_TXT - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Genome data format.
GENOME_DESCRIPTION - Static variable in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
 
GENOME_DESCRIPTION_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
 
GENOME_DESCRIPTION_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
GENOME_FASTA - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Genome data format.
GENOME_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
 
GenomeChecker - Class in fr.ens.biologie.genomique.eoulsan.checkers
This class define a Checker on genome FASTA files.
GenomeChecker() - Constructor for class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
 
GenomeDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define a genome protocol.
GenomeDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol
 
GenomeDescriptionCreator - Class in fr.ens.biologie.genomique.eoulsan.modules.generators
This class define a genome description creator.
GenomeDescriptionCreator() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionCreator
Public constructor.
GenomeDescriptionGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators
This class implements a genome description generator module.
GenomeDescriptionGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
 
GenomeMapperIndexGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators
This class define a module that generate a genome mapper index.
GenomeMapperIndexGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
 
get(Parameter) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.SizeFactorsType
Get the size factors type to be used in DESeq2.
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore
Get some data.
get(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Get the value of metadata entry.
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
get(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
Get the value according the key.
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
get(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType
Get the fit type to be used in DESeq2.
get(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.StatisticTest
Get the statistic test to be used in DESeq2.
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxInfo
Get the value for a key
getAction() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get the action.
getActionArgs() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get the action arguments.
getActions() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ActionService
Get the list of actions available.
getAdditionalAnnotationFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
Get the additional annotation file.
getAdditionalAnnotationFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
 
getAdditionalAnnotationHypertextLinksPath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the additional annotation hypertext links path.
getAdditionalAnnotationStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the additional annotation storage path.
getAlias() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get the alias of the name of the format.
getAlias() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
getAlias() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
getAlignmentFilter(GenericLogger, ReporterIncrementer, String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
Get the ReadAlignmentsFilter object.
getAlignmentsFilterParameters() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
Get the parameters of the read alignments filters.
getAlignmentsFilterParameters() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
Get the parameters of the alignments filter.
getAllDefaultStepId() - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepType
Return the available default step ids of the step types.
getAllFiles(File) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Get all the file on the Rserve server.
getAllFormats() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Get all the registered formats.
getAllModules() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleRegistry
Get all the modules.
getAllSamplesMetadataKeys(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Get all the sample metadata keys of the samples of a design.
getAnnotationClass() - Method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
Get the Eoulsan annotation class that corresponds to the Eoulsan mode.
getArgs() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get command line arguments.
getArgv0() - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
 
getAsBoolean(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
getAsBoolean(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
Get the value according the key as a boolean.
getAsBoolean(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
getAsBoolean(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
getAsList(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
getAsList(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
Get the value according the key as a list.
getAsList(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
getAsList(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
getAuthor() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Get Author.
getAWSAccessKey() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the AWS access key.
getAWSSecretKey() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the AWS secret key.
getBasename() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Get the base name of this DataFile without all its extensions.
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.AdditionalAnnotationDataProtocol
 
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol
 
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol
 
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol
 
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
Get the path where searching the files.
getBogoMips() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo
Get processor bogomips.
getBooleanSetting(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the value of the setting as a boolean value
getBooleanValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
Get the value of the parameter as a boolean value.
getBpipeCommandWrapper() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
Get the path to the Bpipe command wrapper.
getBpipeCommandWrapper() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BundledScriptBpipeTaskScheduler
 
getBpipeCommandWrapper() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.DummyTaskScheduler
 
getBpipeCommandWrapper() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TGCCTaskScheduler
 
getBytesNumberWritten() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream
Get the number of bytes written.
getBytesRead() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
Get the number of bytes read.
getChecker() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module
Get the checker for the module
getChecker() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step
Get Checker.
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
getChecker() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get the checker needed to check data of this type.
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
 
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
 
getCheckersRequired() - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker
Get the list of Checker required to run before this checker.
getCheckersRequired() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
 
getCheckersRequired() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
 
getCheckersRequired() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
 
getCheckersRequired() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
 
getCheckerStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
Get checker step.
getCheckStore() - Static method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore
Get the instance of the CheckStore.
getCheetahScript() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo
Get the Cheetah script.
getClassPath() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get Eoulsan classpath.
getClusterSchedulerName() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the name of the cluster scheduler.
getCommandAuthor() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the command author.
getCommandAuthor() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getCommandAuthor() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getCommandAuthor() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the command author.
getCommandDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get command description.
getCommandDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getCommandDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getCommandDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get command description.
getCommandLine() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus
Get the context command line.
getCommandLine() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
getCommandLine() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult
Gets the command line as a list of string arguments.
getCommandLineAsString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult
Gets the command line as a String.
getCommandLineSettings() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get the command line settings arguments.
getCommandName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the command name.
getCommandName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getCommandName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getCommandName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the command name.
getComment() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Get the comment.
getComparisons() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Get the comparisons DEseq2 option.
getComparisons() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
getCompression() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Get the compression.
getCompression() - Method in interface fr.ens.biologie.genomique.eoulsan.core.OutputPort
Get the compression format of the port.
getCompression() - Method in class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPort
 
getCompressionExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Get the compression extension of this DataFile.
getCompressionLevel() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
Get the compression level to use.
getCompressionsAccepted() - Method in interface fr.ens.biologie.genomique.eoulsan.core.InputPort
Test if the port accept a compressed input format.
getCompressionsAccepted() - Method in class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPort
 
getCompressionType() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Get the compression Type of this DataFile.
getCondition() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
Get the condition.
getCondition() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
 
getCondition() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Get the condition.
getCondition() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
getCondition(Experiment, Sample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Get the Condition metadata value for an experimentSample.
getCondition(ExperimentSample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Get the Condition metadata value for an experimentSample.
getConf() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp
 
getConfiguration() - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
Get Hadoop configuration.
getConfiguration(JobContext) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil
Invoke getConfiguration() method on JobContext.
getConfigurationFileArgument() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get the configuration file argument.
getConfigurationFilePath() - Static method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the configuration file path.
getContentEncoding() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata
Get the content type of the file.
getContentLength() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata
Get the content length of the file.
getContentLength() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
getContentMD5() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata
Get the content MD5 of the file.
getContentType() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata
Get the content type of the file.
getContentType() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get the content type.
getContentType() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
getContentType() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
getContextCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TokenManager
Get the number of context created by the token manager.
getContextCounters(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Get the contextName counters.
getContextCreationTime() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext
Get the creation time of the context.
getContextCreationTime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getContextCreationTime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the creation time of the context.
getContextId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent
Get the context id.
getContextMessage(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Get a context message.
getContextName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext
Get the context name.
getContextName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getContextName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent
Get the context name.
getContrastFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Get the contrastFile DEseq2 option.
getContrastFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
getCores() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo
Get the number of cores of the processor.
getCount() - Method in interface fr.ens.biologie.genomique.eoulsan.modules.fastqc.CounterSequenceFile
Get the count of the read entries.
getCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
 
getCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
 
getCounter(TaskInputOutputContext, String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil
 
getCounterFromEoulsanName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
Get an counter from its HTSeq-count name
getCounterFromHTSeqCountName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
Get an counter from its HTSeq-count name
getCounterGroup() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
Get the counter group to use for this module.
getCounterGroups() - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter
 
getCounterNames(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter
 
getCounters() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus
Get the sample counters.
getCounters() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
getCounterValue(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter
 
getCPUMHz() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo
Get CPU MHz.
getCreationTime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Get the creation time of the job.
getCreationTime() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
getCurrentKey() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
 
getCurrentKey() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
 
getCurrentKey() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
 
getCurrentStep() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the current step.
getCurrentStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getCurrentStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getCurrentValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
 
getCurrentValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
 
getCurrentValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
 
getData(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Create an InputStream from the source.
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
 
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
 
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
 
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
 
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
 
getDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
 
getDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
Get the file as a DataFile.
getDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
getDataFile() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Get the DataFile for an input DataType and a Sample.
getDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
getDataFile(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
 
getDataFile(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
getDataFile(int) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Get the DataFile for an input DataType and a Sample.
getDataFile(MapperInstance, GenomeDescription, Map<String, String>) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage
Get the DataFile that corresponds to a mapper and a genome
getDataFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileStorage
Get a Datafile related to a short name
getDataFileCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
 
getDataFileCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
getDataFileCount() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Count the number for DataFile available for a multi-file DataFormat and a Sample.
getDataFileCount(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
 
getDataFileCount(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
getDataFileCount(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Count the number for DataFile available for a multi-file DataFormat and a Sample.
getDataFilename() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
 
getDataFilename() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
getDataFilename() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Get the pathname for the data.
getDataFilename(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
 
getDataFilename(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
getDataFilename(int) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Get the pathname for the data.
getDataFileParent(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Get the parent source of the source.
getDataFiles(Data) - Static method in class fr.ens.biologie.genomique.eoulsan.core.DataUtils
Get the list of the DataFile objects in a Data object.
getDataFiles(Data) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils
Get the list of the DataFile objects in a Data object.
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Get the DataFormat of the DataFile.
getDataFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata
Get the DataFormat of the file.
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement
Get the data format of the tool element.
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor
 
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor
 
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor
 
getDataFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessor
Get the DataFormat handled by the preprocessor.
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MapperInputPreprocessor
 
getDataFormatForDesignMetadata(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Get the DataFormat that define a metadata entry in the design file.
getDataFormatForSampleMetadata(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Get the DataFormat that define a metadata entry of a sample in the design file.
getDataFormatFromAlias(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Get a DataFormat from its alias.
getDataFormatFromFilename(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Get the DataFormat of a file from its filename
getDataFormatFromFilename(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Get a DataFormat From a file prefix and extension
getDataFormatFromGalaxyFormatName(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Get DataFormat from an Galaxy format name.
getDataFormatFromGalaxyFormatNameOrNameOrAlias(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Get a DataFormat from its Galaxy format name or its name or alias.
getDataFormatFromName(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Get a DataFormat from its name.
getDataFormatFromNameOrAlias(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Get a DataFormat from its alias.
getDataFormatPaths() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the format paths.
getDataFormatsFromExtension(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Get DataFormats from an extension.
getDataName() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Get the data name.
getDataPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Get the data directory path.
getDataRepositoryDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Get the data repository directory.
getDataRepositoryDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the data repository directory.
getDate() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Get the date.
getDefaultClusterMemoryRequired() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the default memory required for the steps in cluster mode.
getDefaultExtension() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get the default extension of the DataType.
getDefaultExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
getDefaultExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
getDefaultFastqFormat() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the default fastq format.
getDefaultProtocol() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
Get the default protocol.
getDefaultStepId() - Method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepType
Get default step id.
getDefaultWorkFile(TaskAttemptContext, String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.CLIMergingAnySAMOutputFormat
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractInfoAction
 
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action
Get action description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecAction
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.IntegrationTestAction
 
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module
Get the description of the module
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus
Get the context description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Get description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get the description of the format.
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Get the description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo
Get the tool description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule
A short description of the tool and what is done in the step.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule
A short description of the tool and what is done in the step.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule
A short description of the tool and what is done in the step.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule
A short description of the tool and what is done in the step.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
 
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
getDesign() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
 
getDesign() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow
Get the design used by the workflow.
getDesign() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment
Get the design related to the experiment.
getDesign() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
getDesign() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample
Get the design related to the sample.
getDesign() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
getDesign(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder
Create design object.
getDesignFile() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the design file path.
getDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the design file.
getDesignFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Get the designFile DEseq2 option.
getDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
getDesignFormatVersion() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.DesignFormatFinderInputStream
Get the format of the data to read.
getDesignMetadataKeyForDataFormat(Design, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Get the field name in a Design object that correspond to a dataformat.
getDesignMetadataKeyName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get the name of the design metadata key of the design file that can provide the DataFile.
getDesignMetadataKeyName() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
getDesignMetadataKeyName() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
getDesignPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Get the design file path.
getDesignReader() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.DesignFormatFinderInputStream
Get the DesignReader for the data.
getDesignStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
 
getDesignStep() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow
Get the design step of the workflow.
getDest() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
 
getDiscardOutput() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
Get the discard output value.
getDispEstFitTypeFromName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType
Get the Dispersion estimation fit type form its name
getDispEstMethodFromName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod
Get the Dispersion estimation method form its name
getDispEstSharingModeFromName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode
Get the Dispersion estimation sharing mode form its name
getDockerBackend() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the Docker backend name.
getDockerConnection() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the Docker connection string.
getDockerConnectionURI() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the Docker connection URI.
getDockerImage() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo
Get Docker image.
getDockerSingularityStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the Docker singularity storage path.
getDoubleSetting(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the value of the setting as a double value
getDoubleValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
Get the value of the parameter as a double value.
getDuration() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskResult
Get the duration of the step.
getDuration() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Get the duration of the step.
getDuration() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
 
getEoulsanDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get Eoulsan directory.
getEoulsanMemory() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get Eoulsan memory requirement.
getEoulsanMode() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
Get the Eoulsan mode of the step.
getEoulsanScriptPath() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get Eoulsan script path.
getErrorMessage() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskResult
Get the error message.
getErrorMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Get the error message.
getErrorMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
 
getException() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskResult
Get the exception.
getException() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Get the exception.
getException() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
 
getException() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult
Gets the exception.
getExecutablePids(String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
Return a set withs pid of existing executable.
getExecutablesTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the temporary directory for executables.
getExecutablesTempDirectoryFile() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the temporary directory File for executables.
getExecutionMode(Class<?>) - Static method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
Get the execution mode related to an annotation class.
getExitCode() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusResult
Return the exit code.
getExitValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult
Gets the exit value.
getExitValue() - Method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessResult
Get the exit value of the process.
getExperiment(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Get the name of an experiment.
getExperiments() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Get the list of the experiments.
getExperimentSample(Sample) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment
Get the experiment sample related to the sample.
getExperimentSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
getExperimentSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
getExperimentSampleAllMetadataKeys(Experiment) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Get all the experiment metadata keys of the samples of a design.
getExperimentSamples() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment
Get experiment samples list.
getExperimentSamples() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
getExperimentSamples() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
getExperimentsUsingASample(Sample) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Get all the experiments related to a sample.
getExpressionCounter() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
Get the counter.
getExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Get the extension of this DataFile without compression extension.
getExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
Get the file extensions of the files to search.
getExtension() - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader
Get the extension of the files to load.
getExtensions() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get the extensions for the DataType
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.AdditionalAnnotationDataProtocol
 
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol
 
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol
 
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol
 
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
Get the list of the file extensions of the files to search.
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
getFastqFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Get the FastqFormat.
getFastqFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Get the fastq format.
getFastqFormat(FastqFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Get the FastqFormat.
getFile() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
 
getFile() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
 
getFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileStorage
Get a file related to a short name
getFile(String, File) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Get a file from the RServer.
getFileAsArray(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Get a file as a byte array.
getFileIndex() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Get the file index.
getFileIndex() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
Get file index.
getFileInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Create an inputStream on a file on RServer.
getFileOutputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Create an outputStream on a file on RServer.
getFilesIntoZip(List<String>, File) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Get a list of files from the RServer.
getFirstPort() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
 
getFirstPort() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports
Get the first port.
getFirstStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
 
getFirstStep() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow
Get the first step of the workflow (after generator steps).
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker
Get format related to the checker.
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
 
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
 
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
 
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
 
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPort
 
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Get the format.
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Port
Get the data format of the port.
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
Get the format of the output
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Get the data format of the data.
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMMerger
 
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMSplitter
 
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionMerger
 
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionSplitter
 
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqMerger
 
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqSplitter
 
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Merger
Get the format related to the splitter.
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMMerger
 
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMSplitter
 
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Splitter
Get the format related to the splitter.
getFullExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Get the base name of this DataFile with all its extensions (include compression extension).
getGalaxyFormatNames() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get the extension from Galaxy tool file of the DataType.
getGalaxyFormatNames() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
getGalaxyFormatNames() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
getGalaxyToolPaths() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the Galaxy tool path.
getGenerator() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get the step needed to generate the DataType from DataTypes provided by the Design file.
getGenerator() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
getGenerator() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
getGenericLogger() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the generic logger.
getGenericLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getGenericLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getGenericLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the generic logger.
getGenericLogger() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
 
getGenomeDescStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the genome description storage path.
getGenomeFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
Get the genome file.
getGenomeFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
 
getGenomeMapperIndexStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the genome mapper index storage path.
getGenomeStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the genome storage path.
getGffFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
Get the GFF file.
getGffFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
 
getGFFStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the GFF storage path.
getGlobalParameters() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Get the globals parameters.
getGtfFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
Get the GTF file.
getGtfFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
 
getGTFStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the GTF storage path.
getHadoopLogLevel() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the Hadoop log level.
getHadoopWorkingDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
Get the Hadoop working directory.
getHadoopWorkingDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the local working directory.
getHadoopWorkingDirectory(TaskContext) - Static method in class fr.ens.biologie.genomique.eoulsan.core.ContextUtils
Get the Hadoop working directory.
getHadoopWorkingPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Get the Hadoop working path.
getHadoopWorkingPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Get the Hadoop working directory.
getHelp() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
Gets the help.
getHelpEoulsanCommand() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get the command used to launch Eoulsan.
getHelpEoulsanCommand() - Method in class fr.ens.biologie.genomique.eoulsan.MainCLI
 
getHelpEoulsanCommand() - Method in class fr.ens.biologie.genomique.eoulsan.MainHadoop
 
getId() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step
Get step id.
getId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
getId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getId() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment
get the experiment id.
getId() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
getId() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample
Get the sample id.
getId() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
getInfoFile() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo
 
getInfoFile() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxInfo
Get the file to parse.
getInfoFile() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxMemInfo
 
getInputData(InputPort) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Get raw access to input data stored in the object.
getInputData(DataFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext
Get the input data for an input DataType and a Sample.
getInputData(DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getInputData(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext
Get the input data for a port name and a Sample.
getInputData(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getInputDataElements() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter
Gets the in data format expected associated with variable found in command line.
getInputPorts() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module
Get the input data format.
getInputPorts() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step
Get the input ports of the step.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule
Define input port.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule
Define input ports.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule
Define input ports.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule
Define input port.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.FilterAndMapReadsHadoopModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterHadoopModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperHadoopModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAM2BAMHadoopModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterHadoopModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
 
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
 
getInputs() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter
Gets the inputs.
getInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
Create an InputStream to load data.
getInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
 
getInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
 
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.actions.ActionService
Retrieve the singleton static instance of an ActionService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskSchedulerService
Retrieve the singleton static instance of an ClusterTaskSchedulerService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.EmergencyStopTasks
Get the singleton instance of the class.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleRegistry
Retrieve the singleton static instance of ModuleRegistry.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepInstances
Singleton method.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry
Get the singleton instance of WorkflowStepObserverRegistry.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowEventBus
Get the singleton instance of WorkflowBusEvent.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Get the singleton instance of DataFormatRegistry
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
Retrieve the singleton static instance of DataProtocolService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.Main
Get the instance of the Main class.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessorService
Retrieve the singleton static instance of an AlignmentsFilter.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.RequirementService
Retrieve the singleton static instance of a RequirementService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.ui.UIService
Retrieve the singleton static instance of UIService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.util.EoulsanDockerManager
Get the instance of the DockerManager.
getInstance(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataMetadataStorage
Get the singleton.
getInstance(DataFile, GenericLogger) - Static method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeDescStorage
Create a GenomeDescStorage
getInstance(String, GenericLogger) - Static method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage
Create a GenomeIndexStorage
getInterpreter(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo
Get the interpreter.
getInterpreterPath() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.GenericExecutorInterpreter
Get the interpreter path.
getIntSetting(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the value of the setting as a integer value
getIntValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
Get the value of the parameter as a integer value.
getIntValueGreaterOrEqualsTo(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
* Get the value of the parameter as a integer value and check if this value is greater or equals to the min parameter value.
getIntValueInRange(int, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
Get the value of the parameter as a integer value and check if this value is in the correct range.
getJarFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the application jar file.
getJarPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
Get the application jar file.
getJarPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Get the application jar path.
getJarPathname(TaskContext) - Static method in class fr.ens.biologie.genomique.eoulsan.core.ContextUtils
Get the application jar file.
getJavaExecutablePath() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get java executable path.
getJavaMailSMTPProperties() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Create a property object for javamail smtp configuration from the settings.
getJobDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the job description.
getJobDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Get the job description.
getJobDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getJobDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getJobDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the job description.
getJobDirectory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the job path.
getJobDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
Get the job directory.
getJobDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Get the job directory.
getJobDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the job path.
getJobDirectory(TaskContext) - Static method in class fr.ens.biologie.genomique.eoulsan.core.ContextUtils
Get the job directory.
getJobEnvironment() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the job environment.
getJobEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Get the job environment.
getJobEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getJobEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getJobEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the job environment.
getJobHost() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the host of the job.
getJobHost() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getJobHost() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getJobHost() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the host of the job.
getJobId() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the job id.
getJobId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Get the job id.
getJobId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getJobId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getJobId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the job id.
getJobPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Get the job path.
getJobUUID() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the UUID of the job.
getJobUUID() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
 
getJobUUID() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getJobUUID() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getJobUUID() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the UUID of the job.
getJVMArgs() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get JVM arguments.
getJVMsPIDs() - Static method in class fr.ens.biologie.genomique.eoulsan.util.locker.LockerUtils
Return a set withs pid of existing JVMs.
getLabel() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
Gets the label.
getLastActiveTime() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
getLastModified() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata
Get the date of the last modification of the file.
getLastModified() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
getLaunchMode() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get the launch mode of the application.
getLaunchScriptPath() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get the path to the launch script.
getLinkedSteps() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPort
 
getLinkedSteps() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Port
Get the steps linked to this port.
getLinksFileFromSettings(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.util.EoulsanTranslatorUtils
Get the links file from the settings.
getLinkTarget() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata
Get the symbolic link target.
getListElements() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
 
getListElements() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
getListElements() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Get the the list of data.
getLocalTempDirectory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get local temporary directory.
getLocalTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getLocalTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getLocalThreadsNumber() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the number of threads to use in Steps computation in local mode.
getLocalWorkingDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
Get the local working directory.
getLocalWorkingDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the local working directory.
getLocalWorkingDirectory(TaskContext) - Static method in class fr.ens.biologie.genomique.eoulsan.core.ContextUtils
Get the local working directory.
getLocalWorkingPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Get the local working path.
getLocalWorkingPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Get the local working directory.
getLogFileArgument() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get the log file argument.
getLogger() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the logger.
getLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the logger.
getLogger() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
Get the logger object.
getLoggerName() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
Get the logger name.
getLogHandler(URI) - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get the Handler to create the log file.
getLogHandler(URI) - Method in class fr.ens.biologie.genomique.eoulsan.MainCLI
 
getLogHandler(URI) - Method in class fr.ens.biologie.genomique.eoulsan.MainHadoop
 
getLogLevelArgument() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Get the log level arguments.
getLowerStringValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
Get the value of the parameter as a lower case String value.
getMapKey(Data) - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
Define the key to use for replicate merging.
getMapKey(Data) - Method in class fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule
 
getMapper() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
Get the mapper.
getMapper() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
Get the mapper object.
getMapperArguments() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
Get the name of the mapper to use.
getMapperArguments() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
Get the arguments of the mapper to use.
getMapperDockerImage() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
Get the mapper Docker image to use.
getMapperFlavor() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
Get the flavor of the mapper to use.
getMapperFlavor() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
Get the flavor of the mapper to use.
getMapperHadoopMemoryRequired() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
Get the amount in MB of memory required to execute the mapper.
getMapperHadoopMemoryRequired() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
Get the amount in MB of memory required to execute the mapper.
getMapperHadoopThreads() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
Get the name of the mapper to use.
getMapperHadoopThreads() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
Get the number of threads to use in local mode.
getMapperLocalThreads() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
Get the number of threads to use in local mode.
getMapperName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
Get the name of the mapper to use.
getMapperName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
Get the name of the mapper to use.
getMapperVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
Get the version of the mapper to use.
getMapperVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
Get the version of the mapper to use.
getMaxFilesCount() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get the maximal number of files used to store data of this format.
getMaxFilesCount() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
getMaxFilesCount() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
getMaxRecordsInRam() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
Get the maximum records in RAM.
getMemTotal() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxMemInfo
Get the total memory of the system.
getMergeableWorkFile(Path, String, String, TaskAttemptContext, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
Returns a name that mergeInto() will recognize as a file to be merged.
getMerger() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get the merger class related to this type.
getMerger() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
getMerger() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
getMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIWorkflowEvent
Get the message of the event.
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
 
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Get metadata about the data.
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Get the design Metadata.
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment
Get the experiment metadata.
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSample
Get the experiment sample metadata.
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl
 
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample
Get the sample metadata.
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataMetadataStorage
Get the metadata of a file.
getMetadata(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Get the metadata for the source.
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
 
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
 
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
 
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
 
getMetadata(Experiment, Sample, String) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Get a metadata value for an experiment and a sample.
getMetadata(ExperimentSample, String) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Get a metadata value for an experimentSample.
getMetaData() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Get the metadata for this DataFile.
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ActionService
 
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskSchedulerService
 
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleService
 
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
 
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessorService
 
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RequirementService
 
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.ui.UIService
 
getMode() - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
Get Eoulsan mode.
getMode() - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
 
getMode() - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
 
getModel() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Get the model DEseq2 option.
getModel() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
getModelColumns(Experiment) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Get the column names used in DESeq2 model.
getModelName() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo
Get the model of processor
getModule() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
Get the underlying Module object.
getModule(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepInstances
Get a module instance.
getModule(Step, String, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepInstances
Get a step instance.
getModuleName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step
Get the module name.
getModuleName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
getModuleName(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Get the module name of the step.
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action
Get the name of the action.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecAction
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.FormatsAction
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.InfoAction
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.IntegrationTestAction
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ModulesAction
 
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker
Get the name of the checker.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GTFChecker
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPort
 
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module
Get the name of the module.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
Get the name of the parameter.
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Port
Get the name of the port.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Get the name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Get data name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Get the name of this DataFile.
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get the name of the format.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.AdditionalAnnotationDataProtocol
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.AnnotationDataProtocol
 
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Get Protocol name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPPathDataProtocol
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPURLDataProtocol
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPPathDataProtocol
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSPathDataProtocol
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSURLDataProtocol
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPURLDataProtocol
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Get design name.
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment
Get the experiment name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample
Get the sample name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
 
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement
Gets the name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter
 
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.ExecutorInterpreter
Get the name of the interpreter.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.GenericExecutorInterpreter
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.Infos.Info
Get the name of the information
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule
Name of the Step.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
Methods
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule
Name of the Step.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule
Name of the Step.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule
Name of the Step.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
 
getName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType
Get the dispersion estimation fitType name
getName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod
Get the dispersion estimation method
getName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode
Get the dispersion estimation sharingMode name
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FirstModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.TerminalModule
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
 
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement
The name of the requirement.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
 
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.ui.UI
Get the name of the UI.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor
 
getName() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
 
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor
Get the name of the RExecutor.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
 
getNote() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
Get the note.
getNote() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent
Get the note.
getNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step
Get the unique numerical identifier of the step.
getNumber() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
getNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Get design number.
getNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment
Get the experiment number.
getNumber() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
getNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample
Get the sample number.
getNumber() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
getOperator() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Get the operator.
getOutputData(DataFormat, Data) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext
Get the output data for an input DataType and a Sample.
getOutputData(DataFormat, Data) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getOutputData(DataFormat, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext
Get the output data for an input DataType and a Sample.
getOutputData(DataFormat, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getOutputData(DataFormat, String, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext
Get the output data for an input DataType and a Sample.
getOutputData(DataFormat, String, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getOutputData(String, Data) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext
Get the output data for a port name and a Sample.
getOutputData(String, Data) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getOutputData(String, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext
Get the output data for a port name and a Sample.
getOutputData(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getOutputData(String, String, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext
Get the output data for a port name and a Sample.
getOutputData(String, String, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getOutputDataElements() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter
Gets the out data format expected associated with variable found in command line.
getOutputDirectory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the output path.
getOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the output directory.
getOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
Get the output directory of the analysis.
getOutputFiles() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
 
getOutputFiles() - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor
Get the output files of the analysis
getOutputFiles() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
 
getOutputPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Get the output path.
getOutputPorts() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module
Get the output data format.
getOutputPorts() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step
Get the output ports of the step.
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule
Define output port.
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule
Define output port.
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
 
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
 
getOutputs() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter
Gets the outputs.
getOutputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
Create an OutputStream to load data.
getOutputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
 
getOutputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
 
getOutputTreeType() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the output tree type.
getParallelizationMode() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module
Get the parallelization mode of the module.
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
Get the parallelization mode of the step.
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
 
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
 
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
 
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
 
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
 
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
 
getParameter(Set<Parameter>, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Get the last parameter which name match for a parameter set.
getParameters() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step
Get the parameter of the step.
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
 
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
 
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
 
getParameters() - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement
Get the parameters of the requirement
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
 
getParent() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Get the parent of this DataFile.
getPart() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Get the file part.
getPart() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
 
getPart() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
getPart() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Get the part of the data.
getPath(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
Get Convert a DataFile object to a Path object.
getPercentComplete() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
 
getPercentComplete() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
 
getPid() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
getPort(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
 
getPort(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports
Get a port.
getPortName() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Get the port name.
getPortName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
Get the port name that produced the file.
getPortNames() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
 
getPortNames() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports
Get the names of the ports
getPortsWithDataFormat(DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
 
getPortsWithDataFormat(DataFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports
Get a list with all the ports that format is the specified format.
getPrefix() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get DataFormat prefix.
getPrefix() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
getPrefix() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
getPriority() - Method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepType
Get the priority of the step.
getProcessesWaiting() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ExecLock
Get the number of processes waiting.
getProcessor() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo
Get the processor name.
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
Get the progress within the split
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
 
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
 
getProgress() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Progress
Get the progress of the context processing.
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
Get the progress of the step.
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent
Get the progress.
getProgressMessage() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Progress
Get the progress message.
getProgressMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
getProtocol() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Get the protocol of this DataFile.
getProtocolPrefixInSource() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Get the prefix of the protocol in the source name of the DataFile.
getRandomId() - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp
 
getRawInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
Create a raw InputStream (without decompression of input data) to load data.
getRawInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
 
getRawInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
 
getRConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Get the R connection.
getReadFilter(GenericLogger, ReporterIncrementer, String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
Get the ReadFilter object.
getReadFilterParameters() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
Get the parameters of the read filters.
getReadFilterParameters() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
Get the parameters of the read filter.
getReads() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Get the reads as a list.
getRecordWriter(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.ExpressionOutputFormat
 
getRecordWriter(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqOutputFormat
 
getRecordWriter(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMOutputFormat
 
getRecordWriter(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.CLIMergingAnySAMOutputFormat
 
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
Get the reducer task count.
getReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Get the reference option.
getReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
Get the reference.
getReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
 
getReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Get the reference.
getReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
getReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
getReference(Experiment, Sample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Get the reference of a sample.
getReference(ExperimentSample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Get the reference of a sample.
getReportName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor
 
getReportName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor
 
getReportName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor
 
getReportName() - Method in interface fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessor
Get the name of the report.
getReportName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MapperInputPreprocessor
 
getRepTechGroup() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
Get the RepTechGroup.
getRepTechGroup() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
 
getRepTechGroup() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Get the RepTechGroup.
getRepTechGroup() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
getRepTechGroup(Experiment, Sample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Get the RepTechGroup metadata value for an experimentSample.
getRepTechGroup(ExperimentSample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Get the Condition metadata value for an experimentSample.
getRequiredEoulsanVersion() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module
Get the required Version of the application to run the Module.
getRequiredEoulsanVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
 
getRequiredMemory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step
Get the required memory for the step.
getRequiredMemory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
getRequiredProcessors() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step
Get the required processors for the step.
getRequiredProcessors() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
getRequiredSteps() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies
Get the required steps.
getRequirements() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module
Get the requirements of the module.
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
 
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
 
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
 
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
 
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
 
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
 
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
 
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
 
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
 
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
 
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
 
getResourceAsStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader
Get the input stream related to a resource.
getResourceAsStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.ClassPathResourceLoader
 
getResourceAsStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader
 
getResourceName(S) - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader
Get the resource name.
getResult() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner
Get the context result.
getResult(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
getResult(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
 
getResult(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
 
getResult(Step) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler
Get the result related to a step.
getResultMail() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the mail address for eoulsan results.
getResultsPanel() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
 
getRootStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
 
getRootStep() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow
Get the first steps of the workflow.
getRServeServerName() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the RServe server name.
getRuntime() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get EoulsanRuntime.
getRuntime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getRuntime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getRuntime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get EoulsanRuntime.
getRuntime() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanRuntime
Get the Eoulsan runtime instance.
getSAMHeaderMerger(Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
Computes the merger of the SAM headers in the files listed in HEADERMERGER_INPUTS_PROPERTY.
getSAMHeaderMerger(Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.HadoopBamUtils
Computes the merger of the SAM headers in the files listed in HEADERMERGER_INPUTS_PROPERTY.
getSample() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
Get the sample that produced the file.
getSample() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSample
Get the experiment sample name.
getSample() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl
 
getSample(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Get the name of a sample.
getSampleId() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Get the sample id related to the data.
getSampleMetadataKeyForDataFormat(Sample, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Get the field name in a Sample object that correspond to a dataformat.
getSampleMetadataKeyName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get the name of the sample metadata key of the design file that can provide the DataFile.
getSampleMetadataKeyName() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
getSampleMetadataKeyName() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
getSampleName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Get the sample name related to the data.
getSampleNumber() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Get the sample number related to the data.
getSampleNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Get the sample number related to the data.
getSamples() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Get the list of the samples.
getSamples() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment
Get the samples of the experiment.
getSamples() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
getSamples() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
getScheduler() - Static method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskSchedulerFactory
Get the scheduler
getSchedulerName() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BundledScriptBpipeTaskScheduler
 
getSchedulerName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler
Get the scheduler name.
getSchedulerName() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.DummyTaskScheduler
 
getSchedulerName() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TGCCTaskScheduler
 
getSerialNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Get the serial number.
getServerName() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Get the name of the Rserve server.
getServiceClasses() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
 
getSetting(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get a setting value.
getSettings() - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
Get Settings.
getSettings() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get Eoulsan settings.
getSettings() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getSettings() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getSettings() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get Eoulsan settings.
getSettings() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanRuntime
Get instance settings.
getSettingsKeyToObfuscated() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get a set with the names of the settings to obfuscate.
getSettingsNames() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get a set of settings names.
getShortName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
Gets the short name.
getShortName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
 
getShortName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
 
getShortName() - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement
Gets the short name.
getSize(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Get the length of a file.
getSMTPHost() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the name of the SMTP server host.
getSource() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Get the source of this DataFile.
getSource() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
getSource() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
Get the source the Galaxy tool.
getSourceAsFile(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Get the underlying File object for the DataFile if the protocol allow it.
getSourceAsFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
getSourceAsFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
 
getSourceFilename(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Get the name of the filename that correspond to the source.
getSplitter() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Get the splitter class related to this type.
getSplitter() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
getSplitter() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
getState() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step
Get the state of the step.
getState() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
getState() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies
Get the state of the step.
getStatus() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent
Get the message type
getStatus(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
getStatus(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
 
getStatus(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
 
getStatus(Step) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler
Get the status related to a step.
getStatusValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusResult
Get status value.
getStderr() - Method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessResult
Get the standard error of the process
getStdout() - Method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessResult
Get the standard output of the process
getStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
Get the workflow step that produced the file.
getStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent
Get the step.
getStep(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
Get the step related to a context.
getStep(TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
Get the step related to a context.
getStepCounters() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Get the step counters.
getStepDataProduct(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Get the data product for the step.
getStepDiscardOutput(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Get the discard output value.
getStepId() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Get Step Id.
getStepIds() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Get the list of step ids.
getStepInputs(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Get the inputs of a step
getStepMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Get step message.
getStepOutputDirectory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the step working directory.
getStepOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
Get step output directory (where output file of the step will be written).
getStepOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getStepOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getStepParameters(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Get the parameters of a step
getStepRequiredMemory(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Get the required memory for the step.
getStepRequiredProcessors(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Get the required processors for the step.
getSteps() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
 
getSteps() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow
Get the steps of the workflow.
getStepVersion() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step
Get the step version required by user.
getStepVersion() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
getStepVersion(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Get the required version of the step.
getStringencyOptHelp() - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
 
getStringValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
Get the value of the parameter as a String value.
getSubmittedTasks() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
Get the number of submitted tasks.
getSubmittedTasks() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent
Get the number of submitted tasks.
getTaskDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the task directory.
getTaskDoneCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
getTaskDoneCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
 
getTaskDoneCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
 
getTaskDoneCount(Step) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler
Get the count of done task contexts of a step.
getTaskFilePrefix() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Create the prefix of a related task file.
getTaskName(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
Get the name of a task.
getTaskOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
Get the task output directory.
getTaskOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Get the task output directory.
getTaskOutputDirectory(TaskContext) - Static method in class fr.ens.biologie.genomique.eoulsan.core.ContextUtils
Get the task output directory.
getTaskPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Get the task path.
getTaskProgress(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
Get the progress of a task.
getTaskRunningCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
getTaskRunningCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
 
getTaskRunningCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
 
getTaskRunningCount(Step) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler
Get the count of running task contexts of a step.
getTaskSubmittedCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
getTaskSubmittedCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
 
getTaskSubmittedCount(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
 
getTaskSubmittedCount(Step) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler
Get the count of submitted task contexts of a step.
getTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
Get the temporary directory.
getTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
 
getTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
 
getTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the temporary directory.
getTempDirectoryFile() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the temporary directory File.
getTemporaryDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
Get the temporary directory.
getTemporaryPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Get the temporary directory path.
getTerminatedTasks() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
Get the number of terminated tasks.
getTerminatedTasks() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent
Get the number of terminated tasks.
getThreadId() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
getThreadsNumber(int, int) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
Get the number of threads to use from localThreads, maxLocalThreads and global threads number.
getTickets(Ticket) - Method in interface fr.ens.biologie.genomique.eoulsan.util.locker.TicketScheduler
Update a ticket by the TicketScheduler and get all the valid tickets.
getTickets(Ticket) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.TicketSchedulerServer
 
getToolElementSelected() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
Gets the tool parameter selected.
getToolElementsResult() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
Gets the tool parameters result.
getToolID() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo
Get the tool Id.
getToolInfo() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter
Gets the tool information.
getToolName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo
Get the tool name.
getToolSource() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo
Get the tool source.
getToolVersion() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo
Get the tool version.
getTotalTaskDoneCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
getTotalTaskDoneCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
 
getTotalTaskDoneCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
 
getTotalTaskDoneCount() - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler
Get the count of done task contexts for the workflow.
getTotalTaskRunningCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
getTotalTaskRunningCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
 
getTotalTaskRunningCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
 
getTotalTaskRunningCount() - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler
Get the count of running task contexts for the workflow.
getTotalTaskSubmittedCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
getTotalTaskSubmittedCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
 
getTotalTaskSubmittedCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
 
getTotalTaskSubmittedCount() - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler
Get the count of submitted task contexts for the workflow.
getTrimmed(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
getTrimmed(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
Get the trimmed value according the key.
getTrimmed(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
getTrimmed(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
getType() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step
Get the type of the step.
getType() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
getType() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
Gets the type.
getUIName() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the UI name.
getUnderLyingData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
Get the underlying Data.
getUploadedDataFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HadoopUploadModule
 
getUploadedDataFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.LocalUploadModule
 
getUploadedDataFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
Generate the DataFile Object for the uploaded DataFile
getUploadedDataFile(DataFile, Step, Sample, String, DataFormat, int) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HadoopUploadModule
 
getUploadedDataFile(DataFile, Step, Sample, String, DataFormat, int) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.LocalUploadModule
 
getUploadedDataFile(DataFile, Step, Sample, String, DataFormat, int) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
Generate the DataFile Object for the uploaded DataFile
getUpperStringValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
Get the value of the parameter as a upper case String value.
getUUID() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Get the UUID.
getValidatedName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
 
getValidatedName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
 
getValidatedName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
 
getValidatedName() - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement
Gets the name which respect Eoulsan's syntax.
getValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
Get the value of the parameter.
getValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement
 
getValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
 
getValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement
 
getValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
 
getValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement
 
getValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement
 
getValue() - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement
Gets the value.
getValues() - Method in class fr.ens.biologie.genomique.eoulsan.Infos.Info
Get the value of the information
getVersion() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module
Get version of the Module.
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule
Version.
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule
Version.
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule
Version.
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule
Version.
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FirstModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
 
getVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.TerminalModule
 
getWorkflow() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step
Get the workflow of the step.
getWorkflow() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext
Get the workflow description
getWorkflow() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
getWorkflow() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getWorkflow() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the workflow description.
getWorkflowContext() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
Get the real Context object.
getWorkflowFile() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext
Get the workflow file path.
getWorkflowFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
 
getWorkflowFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
getWorkflowFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Get the workflow file.
getWorkflowPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Get the workflow file path.
getZooKeeperConnectString() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the ZooKeeper connect string.
getZooKeeperDefaultPort() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the ZooKeeper default port.
getZooKeeperSessionTimeout() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Get the ZooKeeper session timeout.
GFF_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
 
GFFChecker - Class in fr.ens.biologie.genomique.eoulsan.checkers
This class define a Checker on GFF annotation.
GFFChecker() - Constructor for class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
Public constructor.
GFFChecker(boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
Protected constructor.
GFFDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define a annotation protocol.
GFFDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol
 
GFFFastaGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators
This generator allow to generate a genome fasta file from the fasta section of a GFF file.
GFFFastaGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
 
glob() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Get a glob for the filename.
glob(StepOutputPort) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming
Create the glob for the port.
Globals - Class in fr.ens.biologie.genomique.eoulsan
This class contains globals constants for the application.
GOOD_QUALITY_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
GSNAP_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Gmap index data format.
GTF_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
 
GTFChecker - Class in fr.ens.biologie.genomique.eoulsan.checkers
This class define a Checker on GTF annotation.
GTFChecker() - Constructor for class fr.ens.biologie.genomique.eoulsan.checkers.GTFChecker
Public constructor.
GTFDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define a annotation protocol.
GTFDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol
 

H

HADOOP - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
 
HADOOP_COMPATIBLE - fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
 
HADOOP_ONLY - fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
 
HADOOP_PARAMETER_PREFIX - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
 
HADOOP_REDUCER_TASK_COUNT_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
 
HADOOP_TASK - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
 
HADOOP_THREADS_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
HADOOP_TIMEOUT - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
 
HADOOP_TIMEOUT - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
HadoopBamUtils - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
 
HadoopBamUtils() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.HadoopBamUtils
 
HadoopCompatible - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations
This annotation is used to mark a plug-in class as usable in hadoop mode and local mode.
HadoopCompatibleMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.HadoopCompatibleTaskScheduler.HadoopCompatibleMapper
 
HadoopCompatibleTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers
This class is a scheduler for tasks from step with the @HadoopComptible annotation in Hadoop mode.
HadoopCompatibleTaskScheduler.HadoopCompatibleMapper - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers
 
HadoopCompressionCodecs - Class in fr.ens.biologie.genomique.eoulsan.io
This class allow to create input and output stream for compression codec of Hadoop.
HadoopCompressionCodecs() - Constructor for class fr.ens.biologie.genomique.eoulsan.io.HadoopCompressionCodecs
 
HadoopEoulsanRuntime - Class in fr.ens.biologie.genomique.eoulsan
This class define the Runtime to execute low level IO operation for Eoulsan in Hadoop mode.
HadoopExecAction - Class in fr.ens.biologie.genomique.eoulsan.actions
This class launch Eoulsan in hadoop mode.
HadoopExecAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction
 
hadoopInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with Hadoop configuration informations.
HadoopInfo - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop
This class show in log some Hadoop information.
HadoopInfo() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopInfo
 
HadoopJarRepackager - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop
This class allow to repackage the application.
HadoopJobEmergencyStopTask - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop
This class define an EmergencyStopTask for Hadoop Jobs.
HadoopJobEmergencyStopTask(Job) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJobEmergencyStopTask
Public constructor.
HadoopMappingUtils - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class contains utility methods for the Hadoop mapping package classes.
HadoopOnly - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations
This annotation is used to mark a plug-in class as usable in hadoop mode only.
HadoopReporter - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop
This class define a Hadoop reporter.
HadoopReporter(Counters) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter
Constructor.
HadoopReporter(TaskInputOutputContext) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter
Constructor.
HadoopReporterIncrementer - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop
This class define a Hadoop reporter.
HadoopReporterIncrementer(TaskInputOutputContext) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporterIncrementer
Constructor.
HadoopUploadModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload
This class define a module for Hadoop file uploading.
HadoopUploadModule(DataFile, Configuration) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HadoopUploadModule
Public constructor.
halt(int) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
Exit the application.
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.Infos.Info
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJobEmergencyStopTask
 
hashCode() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
hashCode(Object...) - Static method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
hasNext() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
 
hasNext() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
 
hasNextInputStream() - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
Test if there is an other InputStream to concatenate
hasNextInputStream() - Method in class fr.ens.biologie.genomique.eoulsan.io.FileConcatInputStream
 
hasNextInputStream() - Method in class fr.ens.biologie.genomique.eoulsan.io.PathConcatInputStream
 
HDFSDataDownloadModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload
This class define a download module that retrieve data from HDFS at the end of an analysis.
HDFSDataDownloadModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
 
HDFSPathDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define the HDFS protocol in Hadoop mode.
HDFSPathDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
 
HEADERMERGER_INPUTS_PROPERTY - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
 
help(Options) - Method in class fr.ens.biologie.genomique.eoulsan.Main
Show command line help.
HTCondorTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This class define a HTCondor cluster scheduler using a Bpipe script.
HTCondorTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.HTCondorTaskScheduler
Constructor.
HTMLReportArchiveNeigborClass - Class in uk.ac.babraham.FastQC.Report
Empty class for patching the HTMLReportArchive class of FastQC.
HTMLReportArchiveNeigborClass() - Constructor for class uk.ac.babraham.FastQC.Report.HTMLReportArchiveNeigborClass
 
htSeqCountCounterName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
Get the HTSeq-count name of the counter.
HTTPPathDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define the HTTP protocol in Hadoop mode.
HTTPPathDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPPathDataProtocol
 
HTTPSPathDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define the HTTP protocol in Hadoop mode.
HTTPSPathDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSPathDataProtocol
 
HTTPSURLDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define the http protocol in local mode.
HTTPSURLDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSURLDataProtocol
 
HTTPURLDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define the http protocol in local mode.
HTTPURLDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPURLDataProtocol
 

I

IDRModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc
This class defines the IDR quality check step.
IDRModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule
 
ignoreFilteredSequences() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
 
ignoreInReport() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
 
ImportModule - Class in fr.ens.biologie.genomique.eoulsan.modules
This class define a import step.
ImportModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
 
incrCounter(String, String, long) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter
 
incrCounter(String, String, long) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporterIncrementer
 
incrementCounter(Counter, long) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil
 
Info(String, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.Infos.Info
Constructor.
Info(String, int) - Constructor for class fr.ens.biologie.genomique.eoulsan.Infos.Info
Constructor.
Info(String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.Infos.Info
Constructor.
Info(String, String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.Infos.Info
Constructor.
Info(String, List<String>) - Constructor for class fr.ens.biologie.genomique.eoulsan.Infos.Info
Constructor.
Info(String, List<String>, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.Infos.Info
Constructor.
InfoAction - Class in fr.ens.biologie.genomique.eoulsan.actions
This class define an action that show the Eoulsan configuration
InfoAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.InfoAction
 
Infos - Class in fr.ens.biologie.genomique.eoulsan
This class gathers information about Eoulsan configuration and system environment.
Infos() - Constructor for class fr.ens.biologie.genomique.eoulsan.Infos
 
Infos.Info - Class in fr.ens.biologie.genomique.eoulsan
This class define an info.
init(Workflow) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
 
init(Workflow) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
 
init(Workflow) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
 
init(Workflow) - Method in interface fr.ens.biologie.genomique.eoulsan.ui.UI
Initialize the UI.
init(ExpressionCounter, DataFile, DataFile, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterUtils
Initialize the counter.
init(ExpressionCounter, GenomeDescription, DataFile, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterUtils
Initialize the counter.
initConsoleHandler() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
Initialize the console logger handler for Hadoop mappers and reducers.
initConsoleHandler(Level) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
Initialize the console logger handler for Hadoop mappers and reducers.
initEoulsanRuntimeForExternalApp() - Static method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
Initialization Eoulsan runtime for external application who needed Eoulsan
initialize() - Static method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskSchedulerFactory
 
initialize(InputSplit, TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
 
initialize(InputSplit, TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
 
initialize(InputSplit, TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
 
initializeExpressionResults() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.FinalExpressionFeaturesCreator
Clear.
initializeRuntime(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.Main
Initialize the Eoulsan runtime.
initializeRuntime(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.MainCLI
 
initializeRuntime(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.MainHadoop
 
INPUT_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
INPUT_ENTRIES - Static variable in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters
 
INPUT_RAW_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
InputPort - Interface in fr.ens.biologie.genomique.eoulsan.core
This interface define an input port of a step.
InputPorts - Interface in fr.ens.biologie.genomique.eoulsan.core
This interface define a group of input ports.
InputPortsBuilder - Class in fr.ens.biologie.genomique.eoulsan.core
This class allow to easily create input ports for a step.
InputPortsBuilder() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
 
InputPreprocessor - Interface in fr.ens.biologie.genomique.eoulsan.modules.multiqc
This interface define a preprocessor for MultiQC input data.
InputPreprocessorService - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc
This class define a service to retrieve a InputPreprocessor.
install(Progress) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
 
install(Progress) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
 
install(Progress) - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement
Install the requirement.
install(Progress) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
 
INSTALLABLE_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
 
IntegerParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements
This class define an integer tool element parameter.
IntegerParameterToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.IntegerParameterToolElement
Instantiates a new integer tool element parameter.
IntegerParameterToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.IntegerParameterToolElement
Instantiates a new integer tool element parameter.
IntegrationTestAction - Class in fr.ens.biologie.genomique.eoulsan.actions
This class launch integration test with Testng class.
IntegrationTestAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.IntegrationTestAction
 
INTERNET_CHECK_PORT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Port of the server to check internet connection
INTERNET_CHECK_SERVER - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Server name to check internet connection.
INTERPRETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter
 
INTERPRETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter
 
INVALID_CHROMOSOME_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
INVALID_INPUT_PRETREATMENT_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
INVALID_SAM_ENTRIES_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
invalidConfiguration(StepConfigurationContext, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Throw a exception for an invalid configuration.
invalidConfiguration(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Throw a exception for an invalid configuration.
isApplicationAvailableForCurrentArch() - Static method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractAction
Check if the application is available for current platform.
isAvailable() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
 
isAvailable() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
 
isAvailable() - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement
Test if the requirement is available.
isAvailable() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
 
isBuildContrast() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Get the buildContrast DEseq2 option.
isBuildContrast() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
isBypassPlatformChecking() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test if the platform checking must be avoided at Eoulsan startup.
isCache() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
 
isChecker() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Test if a checker is available for this DataFormat.
isChecker() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
isChecker() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
isColorspace() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
 
isColorspace() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
 
isContrast() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Get the contrast DEseq2 option.
isContrast() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
isCopyResultsToOutput() - Method in enum fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput
Test if result must be copied to output.
isCurrentArchCompatible() - Method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractAction
 
isCurrentArchCompatible() - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action
Test if the action can be executed with current platform.
isCurrentArchCompatible() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
 
isCurrentArchCompatible() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
 
isDataFormatFromDesignFile() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Test if the DataFormat is provided by the design file.
isDataFormatFromDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
isDataFormatFromDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
isDataNameValid(String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Test if a data name is valid.
isDebug() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test is the debug mode is enabled.
isDesignChecker() - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker
Test if the Checker is a design checker
isDesignChecker() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
 
isDesignChecker() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
 
isDesignChecker() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
 
isDesignChecker() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
 
isDir() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata
Test if the file is a directory.
isDockerBySingularityEnabled() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Is Docker features are enabled using singularity.
isDockerConnectionDefined() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test if a Docker connection has been set.
isDockerMountNFSRoots() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test if when use Docker, NFS roots must been mounted instead of file paths.
isDoneState() - Method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepState
Test if the state is a done state.
isEmpty() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
 
isEmpty() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports
Test if the object is empty
isEmpty() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
isEmpty() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Test if the number of the elements of the data is equals to 0.
isEmpty() - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
isEmpty() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
Test if there is no metadata.
isEmpty() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
isEmpty() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
isEndOfStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TokenManager
Test if this is the end of the step.
isException() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult
Test if an exception has been thrown.
isExistingDirectoryFile(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Check if a directory exists
isFile(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Check if a file exists
isFilenameValid(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Test if a filename is valid.
isFilenameValid(File) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Test if a filename is valid.
isFilenameValid(String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Test if a filename is valid.
isFinalState() - Method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepState
Test if the state is a final state.
isFormatPrefixValid(String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Test if a format prefix id is valid.
isGenerator() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Test if a generator is available for this DataFormat.
isGenerator() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
isGenerator() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
isGenerator(Module) - Static method in class fr.ens.biologie.genomique.eoulsan.annotations.EoulsanAnnotationUtils
Test if a module contain the @Generator annotation.
isGTFInputFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
Test if GTF input format must be used.
isHadoopCompatible() - Method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
Test if the execution mode is compatible with Hadoop mode.
isHadoopJarMode() - Method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractAction
 
isHadoopJarMode() - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action
Test if the action can be executed in hadoop Jar mode.
isHadoopJarMode() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
 
isHadoopMode() - Method in enum fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
Test if Eoulsan is in an Hadoop mode.
isHadoopProtocolMode() - Method in enum fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
Test if Hadoop protocols can be used in the current Eoulsan mode.
isHidden() - Method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractAction
 
isHidden() - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action
Test if the action must be hidden from the list of available actions.
isHidden() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
 
isImmutable() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Test if the object immutable.
isInstallable() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
 
isInstallable() - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement
Test if the requirement is installable.
isKeepRServeFiles() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test if save.r.keep.files is true
isList() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPort
 
isList() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Port
Test if the port requires a list as value.
isList() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
 
isList() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
isList() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Test if the data is a list.
isLocalCompatible() - Method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
Test if the excution mode is compatible with local mode.
isLocalFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Test if the DataFile use the defaultProtocol.
isMayNotExist() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
 
isMerger() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Test if a merger class is available for this DataFormat.
isMerger() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
isMerger() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
isNoLog(Module) - Static method in class fr.ens.biologie.genomique.eoulsan.annotations.EoulsanAnnotationUtils
Test if a module contain the @NoLog annotation.
isNoObserverRegistered() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry
Test if observers has been registered
isNoOutputDirectory(Module) - Static method in class fr.ens.biologie.genomique.eoulsan.annotations.EoulsanAnnotationUtils
Test if a module contain the @NoOutputDirectory annotation.
isNoTokenToReceive() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TokenManager
Test if there is no token to be received by the token manager.
isObfuscateDesign() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test if design must be obfuscated
isObfuscateDesignRemoveReplicateInfo() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test if replicate information must be removed from design.
isOneFilePerAnalysis() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Test if there is only one file for this DataType per analysis.
isOneFilePerAnalysis() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
isOneFilePerAnalysis() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
isOptional() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
Checks if is optional.
isOptional() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
 
isOptional() - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement
Test if the requirement is optional.
isPairedData(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule
Check if a SAM file contains paired-end data.
isPairedEnd() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Test if the data is paired end data.
isPairedEnd() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
Test if the step works in pair end mode.
isParameterValueValid() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractParameterToolElement
Test if the parameter value is valid
isParameterValueValid() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement
 
isParameterValueValid() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement
 
isParameterValueValid() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.IntegerParameterToolElement
 
isParameterValueValid() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement
 
isParameterValueValid() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement
 
isPortNameValid(String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Test if a port name is valid.
isPrintStackTrace() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test is the debug mode is enabled.
isReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
Get the reference.
isReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
 
isReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Get the reference.
isReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
isRequiredInWorkingDirectory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.InputPort
Test if input data of the port is required in the working directory.
isRequiredInWorkingDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPort
 
isRequiresAllPreviousSteps(Module) - Static method in class fr.ens.biologie.genomique.eoulsan.annotations.EoulsanAnnotationUtils
Test if a module contain the @RequiresPreviousStep annotation.
isRequiresPreviousStep(Module) - Static method in class fr.ens.biologie.genomique.eoulsan.annotations.EoulsanAnnotationUtils
Test if a module contain the @RequiresPreviousStep annotation.
isReuseStepInstance(Module) - Static method in class fr.ens.biologie.genomique.eoulsan.annotations.EoulsanAnnotationUtils
Test if a module contain the @ReuseStepInstance annotation.
isRServeServerEnabled() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test if RServe is enabled.
isRunning() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.SerializableStopwatch
 
isRuntime() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanRuntime
Test if an instance of the runtime is set.
isSameLocalPath(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
Check if two file have the same local path
isSAMOutputFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
Test if SAM output format must be used.
isSaveRscripts() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test if save.r.script is true
isSaveWorkflowImage() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test if an image of the workflow must be saved.
isSendResultMail() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test if an email must be sent at the end of the analysis.
isService(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
 
isSet() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractParameterToolElement
Checks if the value has been set (is not the default value).
isSet() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement
 
isSet() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
Test if the value has been set (if not the default value)
isSet() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement
 
isSet() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement
 
isSetting(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test if a setting key exists.
isSkip() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step
Test if the step must be skipped
isSkip() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
isSkip() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Get the skip option.
isSkip() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
isSkipped(Experiment) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Test if an experiement is skipped.
isSplitable(JobContext, Path) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqInputFormat
 
isSplitable(JobContext, Path) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMInputFormat
 
isSplitter() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat
Test if a splitter class is available for this DataFormat.
isSplitter() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
isSplitter() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
isStarted() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
isStarted() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TokenManager
Test if the thread for the token is started.
isStepIdValid(String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Test if a step id is valid.
isStepSkipped(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Test if the step is skipped.
isStopped() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
isSuccess() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskResult
Test the result of the step is successful.
isSuccess() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Test if the step result is a success.
isSuccess() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
 
isSuccess() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIWorkflowEvent
Test if the event is a success.
isSymbolicLink() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata
Test if the file is a symbolic link.
isTechnicalReplicates(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Test if there is Technical replicates into rRepTechGroup field.
isTerminal(Module) - Static method in class fr.ens.biologie.genomique.eoulsan.annotations.EoulsanAnnotationUtils
Test if a step contain the @Terminal annotation.
isTerminalStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
Test if the step is a terminal step.
isUseBundledBinaries() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
Test if the bundled binaries must be used to perform the step.
isUseOldEoulsanResultFormat() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test if Eoulsan result files must be written using the old format.
isUserDefinedTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test if the temporary directory File has been defined by user.
isUseStandardExternalModules() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Test if standard external modules must be used.
isWorking() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
isWorkingState() - Method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepState
Test if the state is a working state.
ITERATE - fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.SizeFactorsType
 
iterator() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
 

J

JarRepack - Class in fr.ens.biologie.genomique.eoulsan.util
This class allow to repackage a jar file.
JarRepack(File, File) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.JarRepack
Public constructor.
JOB_ID_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Job id constant name.
JOB_PATH_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Logs path constant name.
JOB_UUID_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Job UUID constant name.

K

keySet() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Get the keys of the entries.
keySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
keySet() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
Get the keys of the metadata
keySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
keySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 

L

LANG_ENVIRONMENT_VARIABLE - Static variable in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
 
LanternaUI - Class in fr.ens.biologie.genomique.eoulsan.ui
This class define an UI using Lanterna library.
LanternaUI() - Constructor for class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
 
LATIN1_CHARSET - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets
Latin1 charset.
LATIN1_FILE_ENCODING - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets
Latin1 file encoding.
LAUNCH_MODE_PROPERTY - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Launch mode property.
LAUNCH_SCRIPT_PATH - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Launch script path.
LIBS_TO_HADOOP_REPACK_PROPERTY - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
The name of the system property that contains the list of libraries to repack for hadoop mode.
LICENSE_TXT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Licence text.
LinuxCpuInfo - Class in fr.ens.biologie.genomique.eoulsan.util
Get information about processor on Linux systems.
LinuxCpuInfo() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo
Public constructor.
LinuxInfo - Class in fr.ens.biologie.genomique.eoulsan.util
This class define a linux info file parser.
LinuxInfo() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.LinuxInfo
 
LinuxMemInfo - Class in fr.ens.biologie.genomique.eoulsan.util
Get information about memory on Linux systems
LinuxMemInfo() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.LinuxMemInfo
Public constructor.
list() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
List the content of a directory.
list() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
list(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
List a directory.
list(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
list(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
 
listFiles() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
List files on Rserve server.
listPathsByPrefix(Path, String, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Return a list of the file of a path
listPathsByPrefix(Path, String, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Return a list of the file of a path
listPathsBySuffix(Path, String, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Return a list of the file of a path
listPathsBySuffix(Path, String, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Return a list of the file of a path
load(InputStream, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader
Load a resource.
loadAllResources() - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader
 
loadAllResources() - Method in interface fr.ens.biologie.genomique.eoulsan.util.ResourceLoader
Load all available resources.
loadImage(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Load an image.
loadMetadata(Data) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataMetadataStorage
Set the metadata of a data from the metadata storage.
loadMetadata(Data, List<DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataMetadataStorage
Set the metadata of a data from the metadata storage.
loadModule(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleRegistry
Load a module.
loadPreResults(File) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.FinalExpressionFeaturesCreator
Load pre result file.
loadPreResults(InputStream) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.FinalExpressionFeaturesCreator
Load pre-result file.
loadResources(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader
 
loadResources(String) - Method in interface fr.ens.biologie.genomique.eoulsan.util.ResourceLoader
Load a resource.
loadSAMHeaders(JobContext) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils
Load SAM headers.
loadSettings() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Load application options.
loadSettings(File) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Load application options.
loadTranslator(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.util.EoulsanTranslatorUtils
Create a translator annotation from a link file.
loadTranslator(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.util.EoulsanTranslatorUtils
Create a translator annotation from an additional annotation file and a link file.
LOCAL - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
 
LOCAL - fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType
 
LOCAL - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType
 
LOCAL_ONLY - fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
 
LOCAL_THREADS_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
LocalEoulsanRuntime - Class in fr.ens.biologie.genomique.eoulsan
This class define the Runtime to execute low level IO operation for Eoulsan in local mode.
LocalOnly - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations
This annotation is used to mark a plug-in class as usable in local mode only.
LocalUploadModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload
This class define a Step for local mode file uploading.
LocalUploadModule(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.LocalUploadModule
Public constructor.
lock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock
 
lock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLocker
 
lock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ExecFileLock
 
lock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ExecLock
 
lock() - Method in interface fr.ens.biologie.genomique.eoulsan.util.locker.Locker
Wait the token and then lock the resource.
lock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.TicketLocker
 
lock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ZooKeeperLocker
 
Locker - Interface in fr.ens.biologie.genomique.eoulsan.util.locker
This interface define an interface for the global execution locker.
LockerUtils - Class in fr.ens.biologie.genomique.eoulsan.util.locker
Utility class for the locker classes.
LockerUtils() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.LockerUtils
 
log(Level, Infos.Info) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Log a list of Info.
log(Level, List<Infos.Info>) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Log a list of Info.
LOG_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Log extension.
LOG_FILENAME - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Eoulsan log filename.
LOG_FORMATTER - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Format of the log.
LOG_LEVEL - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
The log level of the application.
logConfig(String) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
Log a CONFIG message using getLogger().config().
logEndTime(Process, String, long) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
Log the time of execution of a process.
logFiner(String) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
Log a FINER message using getLogger().finer().
logFinest(String) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
Log a FINEST message using getLogger().finest().
logHadoopSysInfo() - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopInfo
 
logInfo(String) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
Log an INFO message using getLogger().info().
logPath(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Create the log path.
logSettings() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Add all the settings to the log.
logSevere(String) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
Log an SEVERE message using getLogger().severe().
logWarning(String) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
Log an WARNING message using getLogger().warning().
LOW_QUAL_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
LRT - fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.StatisticTest
 

M

MACS2_RMODEL - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.ChIPSeqDataFormats
MACS 2 R model format.
MACS2Module - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling
This class defines the macs2 peak-calling step.
MACS2Module() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
 
mailInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with email configuration informations.
main(String[]) - Static method in class fr.ens.biologie.genomique.eoulsan.Main
Main method of the program.
main(String[]) - Static method in class fr.ens.biologie.genomique.eoulsan.util.locker.TicketLocker
Main method.
Main - Class in fr.ens.biologie.genomique.eoulsan
This class is the main class.
MainCLI - Class in fr.ens.biologie.genomique.eoulsan
Main class in local mode.
MainCLI(String[]) - Constructor for class fr.ens.biologie.genomique.eoulsan.MainCLI
Constructor.
MainHadoop - Class in fr.ens.biologie.genomique.eoulsan
Main class in Hadoop mode.
MainHadoop(String[]) - Constructor for class fr.ens.biologie.genomique.eoulsan.MainHadoop
Constructor.
makeOptions() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Create options for command line
makeOptions() - Method in class fr.ens.biologie.genomique.eoulsan.MainCLI
Create options for command line
makeReport(HTMLReportArchive) - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
 
map(LongWritable, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.HadoopCompatibleTaskScheduler.HadoopCompatibleMapper
 
map(LongWritable, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionMapper
 
map(LongWritable, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentMapper
'key': offset of the beginning of the line from the beginning of the TFQ file.
map(LongWritable, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DataFileDistCp.DistCpMapper
 
map(Text, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionMapper
'key': offset of the beginning of the line from the beginning of the alignment file.
map(Text, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionSAMOutputMapper
'key': offset of the beginning of the line from the beginning of the alignment file.
map(Text, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterMapper
'key': offset of the beginning of the line from the beginning of the TFQ file.
map(Text, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperMapper
'key': offset of the beginning of the line from the beginning of the TFQ file.
map(Text, Text, Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterMapper
'key': offset of the beginning of the line from the beginning of the SAM file if data are in single-end mode or in TSAM file if data are in paired-end mode.
MAPPER_ARGUMENTS_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
MAPPER_DOCKER_IMAGE_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
MAPPER_FLAVOR_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
MAPPER_INDEX_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
 
MAPPER_INDEX_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
MAPPER_NAME_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
MAPPER_RESULT_BED - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
BED format.
MAPPER_RESULTS_BAM - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
BAM results data format.
MAPPER_RESULTS_INDEX_BAI - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
BAM index results data format.
MAPPER_RESULTS_LOG - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Mapper log file format.
MAPPER_RESULTS_SAM - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
SAM results data format.
MAPPER_VERSION_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
MAPPER_WRITING_ERRORS - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
MapperIndexDataFormat - Class in fr.ens.biologie.genomique.eoulsan.data
This class define a DataFormat from an XML file.
MapperIndexDataFormat(Mapper) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
Public constructor.
MapperIndexDataFormat(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
Public constructor.
MapperInputPreprocessor - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc
This class define a preprocessor for mapper reports.
MapperInputPreprocessor() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MapperInputPreprocessor
 
MappingCounters - Enum in fr.ens.biologie.genomique.eoulsan.modules.mapping
This enum define the names of the counters of the steps of this package.
MapReduceUtils - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop
This class contains utility method to easily manipulate the new Hadoop MapReduce API.
markSupported() - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
 
MatrixToCellRangerMatrixModule - Class in fr.ens.biologie.genomique.eoulsan.modules.singlecell
This class define a class that allow to create a Cell Ranger matrix from an existing matrix file.
MatrixToCellRangerMatrixModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
 
MAX_LINE_LENGTH - Static variable in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
 
MAX_LOCAL_THREADS_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
MAX_READS_TO_CHECK - Static variable in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
 
MaxByteInputStream - Class in fr.ens.biologie.genomique.eoulsan.io
This class allow to create an InputStream that can read a maximum of byte from another InputStream.
MaxByteInputStream(InputStream, long) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.MaxByteInputStream
Public constructor
MAXIMUM - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode
 
maxValueLength() - Method in class fr.ens.biologie.genomique.eoulsan.Infos.Info
Get the maximal length of the values
MEAN - fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType
 
memInfo() - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with memory informations.
merge(Iterator<DataFile>, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMMerger
 
merge(Iterator<DataFile>, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionMerger
 
merge(Iterator<DataFile>, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqMerger
 
merge(Iterator<DataFile>, DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Merger
Merger data.
merge(Iterator<DataFile>, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMMerger
 
MergeInputRepLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq
This class merges SAM files of input of the same experiment.
MergeInputRepLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule
 
mergeInto(OutputStream, Path, String, String, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
Merges the files in the given directory that have names given by getMergeableWorkFile() into out.
mergeInto(OutputStream, Path, String, String, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.HadoopBamUtils
Merges the files in the given directory that have names given by getMergeableWorkFile() into out.
MergePeaksModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling
This class defines the peak merging step.
MergePeaksModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
 
Merger - Interface in fr.ens.biologie.genomique.eoulsan.splitermergers
This interface define a splitter.
MergerModule - Class in fr.ens.biologie.genomique.eoulsan.modules
This class define a generic merger module.
MergerModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
 
mergeSAMInto(Path, Path, String, String, SAMFormat, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
Merges the files in the given directory that have names given by getMergeableWorkFile() into out in the given SAMFormat, using getSAMHeaderMerger().getMergedHeader() as the header.
mergeSAMInto(Path, Path, String, String, SAMFormat, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.HadoopBamUtils
Merges the files in the given directory that have names given by getMergeableWorkFile() into out in the given SAMFormat, using getSAMHeaderMerger().getMergedHeader() as the header.
Metadata - Interface in fr.ens.biologie.genomique.eoulsan.design
This interface defines common methods for metadata.
MINIMAL_JAVA_VERSION_REQUIRED - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Minimal java version required by Eoulsan.
MINIMAP2_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Minimap2 index data format.
Minimap2IndexGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators
This class define a module that generate a Minimap2 mapper index.
Minimap2IndexGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
 
MISSING_MATES_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
mkdir() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Create a directory with the path of the DataFile.
mkdir(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Create a directory.
mkdir(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
mkdir(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
 
mkdirs() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Create a directory and its parents if not exists with the path of the DataFile.
mkdirs(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Create a directory and its parents if not exists.
mkdirs(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
mkdirs(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
 
mkdirs(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Create a directory.
MODEL_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
 
Module - Interface in fr.ens.biologie.genomique.eoulsan.core
This interface define a Module.
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.FirstModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
Module name.
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
Module name.
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule
 
MODULE_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.TerminalModule
 
ModuleRegistry - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a registry for modules.
Modules - Class in fr.ens.biologie.genomique.eoulsan.core
This class contains useful methods for writing Step classes.
ModulesAction - Class in fr.ens.biologie.genomique.eoulsan.actions
This class define an action that show the list of available formats.
ModulesAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ModulesAction
 
modulesAndFormatsInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with modules and format informations.
ModuleService - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class allow to get a Step object from a class in the classpath.
MonoThreadTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers
This class define a mono thread scheduler.
MonoThreadTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.MonoThreadTaskScheduler
 
move(Path, Path, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Move file from a path to another path.
move(Path, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Move file from a path to another path.
MULTIQC_REPORT_HTML - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
MultiQC HTML report format.
MultiQCModule - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc
This class define a module for MultiQC.
MultiQCModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
 
MultiThreadTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers
This class define a muti thread scheduler.
MultiThreadTaskScheduler(int) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.MultiThreadTaskScheduler
Constructor.

N

name() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
 
name() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
 
name() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
 
NAME_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
 
Naming - Class in fr.ens.biologie.genomique.eoulsan.core
This class contains methods to validate workflow object names.
needAdditionalRecordAfterSplit() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.CompressedSplitFastqLineReader
 
newDataPath(DataPath, String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeDescStorage
 
newDataPath(DataPath, String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage
 
newDataPath(DataPath, String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileStorage
 
newDataPath(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeDescStorage
 
newDataPath(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage
 
newDataPath(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileStorage
 
newDockerRequirement(String) - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
Create a new docker image as mandatory requirement.
newDockerRequirement(String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
Create a new docker image requirement.
newEoulsanException(ToolInfo, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Create an EoulsanException.
newEoulsanException(ToolInfo, String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Create an EoulsanException.
newEoulsanRuntime(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
Public constructor, initialize the runtime.
newEoulsanRuntime(Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
Public constructor, initialize the runtime.
newGenericCounter(String, String, long) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil
 
newJobContext(Configuration, JobID) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil
Creates JobContext from a JobConf and jobId using the correct constructor for based on Hadoop version.
newPathRequirement(String) - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
Create a new mandatory executable requirement.
newPathRequirement(String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
Create a new executable requirement.
newPathWithOtherExtension(Path, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Create a new path with the same parent directory and basename but without another extension.
newRExecutor(RExecutorFactory.Mode, String, String, File, File) - Static method in class fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory
Create a new instance of RExecutor.
newRserveRequirement(String) - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
Create a new mandatory Rserve requirement.
newRserveRequirement(String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
Create a new Rserve requirement.
newServer(Set<Ticket>, String, int) - Static method in class fr.ens.biologie.genomique.eoulsan.util.locker.TicketSchedulerServer
 
newService(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
 
newSimpleProcess() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.AbstractExecutorInterpreter
Create a new SimpleProcess that will be use to launch the command.
newSimpleProcess() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter
 
newStandardFilename(Step, String, DataFormat, Sample, int, CompressionType) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
Create a standard filename.
newTaskAttemptContext(Configuration, TaskAttemptID) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil
Creates TaskAttempContext from a JobConf and jobId using the correct constructor for based on Hadoop version.
newToolElement(ToolInfo, Element) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElementFactory
Gets the instance tool element.
newToolElement(ToolInfo, Element, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElementFactory
Gets the instance tool element.
next() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
 
next() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
 
nextInputStream() - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
Get the next InputStream to concatenate
nextInputStream() - Method in class fr.ens.biologie.genomique.eoulsan.io.FileConcatInputStream
 
nextInputStream() - Method in class fr.ens.biologie.genomique.eoulsan.io.PathConcatInputStream
 
nextKeyValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
 
nextKeyValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
 
nextKeyValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
 
nextKeyValue(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
 
NO - fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput
 
NO_HDFS_DOWNLOAD - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
Key in the settings to use to disable the downloads.
noInputPort() - Static method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Create the ports with no ports.
NoLog - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations
This annotation is used to mark a step class that requires no log.
NONE - fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
 
NoOutputDirectory - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations
This annotation is used to mark a step class that requires no output directory.
noOutputPort() - Static method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder
Create the ports with no ports.
Normalization - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana
This class create and launch an R script to compute normalisation of expression data
Normalization(RExecutor, Design) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Public constructor.
NORMALIZATION_FUNCTIONS - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
 
NormalizationModule - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana
This class define the module for normalization
NormalizationModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
 
NOT_ALIGNED_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
NOT_NEEDED - fr.ens.biologie.genomique.eoulsan.core.ParallelizationMode
 
NOT_UNIQUE_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
notifyStepState(Step, int, int, double) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver
The progress of the step has been changed.
notifyStepState(Step, int, int, double) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
 
notifyStepState(Step, int, int, double) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
 
notifyStepState(Step, int, int, double) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
 
notifyStepState(Step, int, String, double) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver
The progress of the step for a sample has been changed.
notifyStepState(Step, int, String, double) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
 
notifyStepState(Step, int, String, double) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
 
notifyStepState(Step, int, String, double) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
 
notifyStepState(Step, Step.StepState) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver
The status of the step has been changed.
notifyStepState(Step, Step.StepState) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
 
notifyStepState(Step, Step.StepState) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
 
notifyStepState(Step, Step.StepState) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
 
notifyStepState(Step, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver
The note of the step has been changed.
notifyStepState(Step, String) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
 
notifyStepState(Step, String) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
 
notifyStepState(Step, String) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
 
notifyTaskDone(Step, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver
Notify that a task has been done.
notifyTaskDone(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
 
notifyTaskDone(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
 
notifyTaskDone(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
 
notifyTaskRunning(Step, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver
Notify that a task is running.
notifyTaskRunning(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
 
notifyTaskRunning(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
 
notifyTaskRunning(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
 
notifyTaskSubmitted(Step, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver
Notify that a task has been submitted.
notifyTaskSubmitted(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
 
notifyTaskSubmitted(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
 
notifyTaskSubmitted(Step, int) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
 
notifyWorkflowSuccess(boolean, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserver
Notify the success of the workflow.
notifyWorkflowSuccess(boolean, String) - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
 
notifyWorkflowSuccess(boolean, String) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
 
notifyWorkflowSuccess(boolean, String) - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
 
NoUI - Class in fr.ens.biologie.genomique.eoulsan.ui
This class define an UI that do nothing.
NoUI() - Constructor for class fr.ens.biologie.genomique.eoulsan.ui.NoUI
 
nullToEmpty(Collection<E>) - Static method in class fr.ens.biologie.genomique.eoulsan.util.CollectionUtils
Return an empty collection if the input collection is null;

O

obfuscate(Design, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Remove optional description fields and obfuscate condition field.
OBFUSCATE_DESIGN_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Obfuscate design default.
OBFUSCATE_DESIGN_REMOVE_REPLICATE_INFO_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Remove design replicate info when obfuscate design default.
onResized(Terminal, TerminalSize) - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
 
open() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Create an InputStream for the DataFile.
open() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
openConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
 
openConnection() - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor
Open the connection.
openConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
 
openDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Open the design file.
openFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Open a file to read on Rserve server.
openParamFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Open the Workflow file.
OPERATOR_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
 
OPTIONAL_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
 
OTHER_LOG_FILENAME - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Other log filename.
OtherLogConfigurator - Class in fr.ens.biologie.genomique.eoulsan
This class allow to configure non Eoulsan log using Log4J.
OtherLogConfigurator() - Constructor for class fr.ens.biologie.genomique.eoulsan.OtherLogConfigurator
 
OUTPUT_COMPRESSION_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
 
OUTPUT_COMPRESSIONS_ALLOWED_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
 
OUTPUT_FILE_FORMAT_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
 
OUTPUT_FILTERED_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
OUTPUT_FILTERED_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
OUTPUT_MAPPING_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
OUTPUT_PATH_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Output path constant name.
OUTPUT_PRETREATMENT_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
OUTPUT_TREE_TYPE_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Output tree type.
OutputPort - Interface in fr.ens.biologie.genomique.eoulsan.core
This interface define an output port of a step.
outputPortName - Variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser.StepOutputPort
 
OutputPorts - Interface in fr.ens.biologie.genomique.eoulsan.core
This interface define a group of output ports.
OutputPortsBuilder - Class in fr.ens.biologie.genomique.eoulsan.core
This class allow to easily create input ports for a step.
OutputPortsBuilder() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder
 
OWN_PARALLELIZATION - fr.ens.biologie.genomique.eoulsan.core.ParallelizationMode
 

P

PAIRED_END_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
 
PairedEndFastqToTfq - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class allow to convert two FASTQ file in one TFQ file.
PairedEndFastqToTfq() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PairedEndFastqToTfq
 
PairedEndFastqToTfq.FastqPairedEndReducer - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class define the reducer required to convert FASTQ files into TFQ file.
ParallelizationMode - Enum in fr.ens.biologie.genomique.eoulsan.core
This enum define the parallelization modes of a step.
Parameter - Class in fr.ens.biologie.genomique.eoulsan.core
This class define a parameter.
Parameter(String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.Parameter
Public constructor.
PARAMETER_PREFIX - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
The prefix of the parameters of the application.
PARAMETRIC - fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType
 
PARAMETRIC - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType
 
PARENT_ID_NOT_FOUND_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
PARENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
parse() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Parse the workflow file.
parse() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxInfo
 
parse(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Create a FileNaming object from a DataFile object.
parse(File) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Create a FileNaming object from a File object.
parse(String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Create a FileNaming object from a filename.
parse(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput
This method define a parser for the values of the "discardoutput" attribute of the Eoulsan workflow.
parse(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory.Mode
Parse a mode name and returns the mode.
parseRExecutorParameter(StepConfigurationContext, Set<Parameter>, Set<Requirement>, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration
Parse the step parameter and create a configured RExecutor object.
PARTIALLY_DONE - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
 
partitionInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with Docker configuration informations.
patchFastQC() - Static method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCRuntimePatcher
Patch FastQC for hadoop mode.
PathConcatInputStream - Class in fr.ens.biologie.genomique.eoulsan.io
This class define an InputStream that concatenate path in an InputStream.
PathConcatInputStream(List<Path>, Configuration) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.PathConcatInputStream
Constructor.
PathDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define an abstract class for DataProtocols based on the Hadoop framework Path object.
PathDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
Constructor.
PathRequirement - Class in fr.ens.biologie.genomique.eoulsan.requirements
This class define a executable requirement.
PathRequirement() - Constructor for class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
 
PathUtils - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop
This class define utility method to manipulate the Hadoop Path object.
PathUtils.PrefixPathFilter - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop
Simple PathFilter to filter Paths with their beginning
PathUtils.SuffixPathFilter - Class in fr.ens.biologie.genomique.eoulsan.util.hadoop
Simple PathFilter to filter Paths with their suffix
PausableThreadPoolExecutor - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers
This class define a Pausable thread pool executor.
PausableThreadPoolExecutor(int) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.PausableThreadPoolExecutor
public constructor.
pause() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MultiThreadTaskScheduler
 
pause() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.PausableThreadPoolExecutor
Pause the executor.
PBSProTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This class define a PBSPro cluster scheduler using a Bpipe script.
PBSProTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.PBSProTaskScheduler
Constructor.
PEAK - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.ChIPSeqDataFormats
Peak format data format.
PEAK_XLS - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.ChIPSeqDataFormats
Peaks XLS format.
PER_CONDITION - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod
 
POOLED - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod
 
Port - Interface in fr.ens.biologie.genomique.eoulsan.core
This interface define a port of a step.
Ports<E extends Port> - Interface in fr.ens.biologie.genomique.eoulsan.core
This interface define a group of ports.
PORTS_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
 
PrefixPathFilter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils.PrefixPathFilter
Public constructor.
PrefixPathFilter(String, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils.PrefixPathFilter
Public constructor.
preprocess(TaskContext, Data, File) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor
 
preprocess(TaskContext, Data, File) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor
 
preprocess(TaskContext, Data, File) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor
 
preprocess(TaskContext, Data, File) - Method in interface fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessor
Preprocess data.
preprocess(TaskContext, Data, File) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MapperInputPreprocessor
 
PreTreatmentExpressionMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop
This class define a mapper for the pretreatment of paired-end data before the expression estimation step.
PreTreatmentExpressionMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionMapper
 
PreTreatmentExpressionReducer - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop
This class define a reducer for the pretreatment of paired-end data before the expression estimation step.
PreTreatmentExpressionReducer() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionReducer
 
PreTreatmentMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class defines a mapper for the pretreatment of paired-end data before the reads filtering step.
PreTreatmentMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentMapper
 
PreTreatmentReducer - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class define a reducer for the pretreatment of paired-end data before the reads filtering step.
PreTreatmentReducer() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentReducer
 
PRINT_STACK_TRACE_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Print stack trace default.
printWarning(String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
Print warning.
printWrapped(PrintStream, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
 
printWrapped(PrintStream, String, int) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
 
printWrapped(PrintStream, String, int, int) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
 
process(WatchedEvent) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLocker
 
process(WatchedEvent) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ZooKeeperLocker
 
PROCESS - fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory.Mode
 
ProcessRExecutor - Class in fr.ens.biologie.genomique.eoulsan.util.r
This class define a standard RExecutor using a system process.
ProcessRExecutor(File, File) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
Constructor.
processSequence(Sequence) - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
 
ProcessThreadErrOutput(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessThreadErrOutput
 
ProcessThreadOutput(InputStream, OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler.ProcessThreadOutput
Constructor.
ProcessUtils - Class in fr.ens.biologie.genomique.eoulsan.util
Utility class for launching external process.
ProcessUtils.ProcessResult - Class in fr.ens.biologie.genomique.eoulsan.util
 
ProcessUtils.ProcessThreadErrOutput - Class in fr.ens.biologie.genomique.eoulsan.util
This class allow to fetch standard error of the process, without printing
Progress - Interface in fr.ens.biologie.genomique.eoulsan.core
This interface allow to set the progress of a task.
ProgressCounterInputStream - Class in fr.ens.biologie.genomique.eoulsan.io
This class implements a FilterInputStream that inform Hadoop of the progress of task using counters.
ProgressCounterInputStream(InputStream, Counter) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterInputStream
 
ProgressCounterOutputStream - Class in fr.ens.biologie.genomique.eoulsan.io
This class implements an OutputStream that inform Hadoop of the progress of task using counters.
ProgressCounterOutputStream(OutputStream, Counter) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterOutputStream
 
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.AnnotationDataProtocol
 
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPPathDataProtocol
Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPURLDataProtocol
Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol
Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol
 
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol
 
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPPathDataProtocol
Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSPathDataProtocol
Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSURLDataProtocol
Protocol name.
PROTOCOL_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPURLDataProtocol
Protocol name.
publish(LogRecord) - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler
 
put(MapperInstance, GenomeDescription, Map<String, String>, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage
Put the index archive in the storage.
putData(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Create an OutputStream from the source.
putData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
 
putData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
putData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
 
putData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
 
putData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
 
putData(DataFile, DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Copy data from a source to a destination source
putData(DataFile, DataFileMetadata) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Create an OutputStream from the source.
putFile(DataFile, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
Put a file for the analysis.
putFile(DataFile, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor
 
putFile(DataFile, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
 
putFile(DataFile, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
 
putFile(File, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Put a file from the RServer.
putFile(InputStream, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Put a file from the RServer.
putInputFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
 
putInputFile(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor
Put a file for the analysis.
putInputFile(DataFile, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
 
putInputFile(DataFile, String) - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor
Put a file.
PYTHON_VARIABLES_DICT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter
The Constant INSTANCE_NAME.

R

raisesError() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
 
raisesWarning() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
 
rAndRserveInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with R and Rserve configuration informations.
RATIO - fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.SizeFactorsType
 
rawCopy(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.data.DataFiles
Copy a file.
rawCreate() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Create an OutputStream for the DataFile.
rawCreate() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
rawOpen() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Create an InputStream for the DataFile.
rawOpen() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
rConnection - Variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
 
rConnection - Variable in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
 
read() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.DefaultDesignReader
 
read() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.DesignFormatFinderInputStream
 
read() - Method in interface fr.ens.biologie.genomique.eoulsan.design.io.DesignReader
Read the design.
read() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignReader
 
read() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignReader
 
read() - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
 
read() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
 
read() - Method in class fr.ens.biologie.genomique.eoulsan.io.MaxByteInputStream
 
read() - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterInputStream
 
read(byte[]) - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
 
read(byte[]) - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
 
read(byte[]) - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterInputStream
 
read(byte[], int, int) - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
 
read(byte[], int, int) - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
 
read(byte[], int, int) - Method in class fr.ens.biologie.genomique.eoulsan.io.MaxByteInputStream
 
read(byte[], int, int) - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterInputStream
 
read(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Read a step result file.
read(InputStream) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Read a step result file.
readAndCheckDesign(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Read and Check design
readLine(Text, int, int) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.CompressedSplitFastqLineReader
 
READS_FASTQ - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Reads fastq data format.
READS_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
 
READS_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
 
READS_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
READS_REJECTED_BY_FILTERS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
READS_TFQ - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Reads tfq data format.
ReadsChecker - Class in fr.ens.biologie.genomique.eoulsan.checkers
This class define a checker on FASTQ files.
ReadsChecker() - Constructor for class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
 
ReadsFilterHadoopModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class is the main class for the filter reads program in hadoop mode.
ReadsFilterHadoopModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterHadoopModule
 
ReadsFilterLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local
This class define a module for reads filtering.
ReadsFilterLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsFilterLocalModule
 
ReadsFilterMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class defines a read filter mapper.
ReadsFilterMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterMapper
 
ReadsMapperHadoopModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class define an mapper module in Hadoop mode.
ReadsMapperHadoopModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperHadoopModule
 
ReadsMapperLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local
This class define a module for reads mapping.
ReadsMapperLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
 
ReadsMapperMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class defines a generic mapper for reads mapping.
ReadsMapperMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperMapper
 
readStaticScript(String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Read a static part of the generated script.
READY - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
 
reduce(Text, Iterable<LongWritable>, Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionReducer
'key': annotation identifier of the feature (gene, mRNA, exon...).
reduce(Text, Iterable<Text>, Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionReducer
'key': the identifier of the aligned read without the integer indicating the member of the pair.
reduce(Text, Iterable<Text>, Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PairedEndFastqToTfq.FastqPairedEndReducer
 
reduce(Text, Iterable<Text>, Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentReducer
'key': the identifier of the read without the integer indicating the member of the pair.
reduce(Text, Iterable<Text>, Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterReducer
'key': identifier of the aligned read, without the integer indicating the pair member if data are in paired-end mode.
REFERENCE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
 
REFERENCE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
 
REFERENCE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
 
referenceValueToInt(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Convert a reference value to an integer.
register(AbstractStep) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
Register a step of the workflow.
register(DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Register a DataFormat.
register(DataFormat[]) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Register DataFormats.
register(Object) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowEventBus
Register an listener object.
registerInputAndOutputPorts(Module) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
 
registerStep(Step, Module) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepInstances
Register a step instance.
registerThreadGroupLogger(ThreadGroup, Logger) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
Register a logger for a thread group.
reload() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleRegistry
Reload the list of available modules.
reload() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry
Reload the list of the available data types.
reload() - Method in class fr.ens.biologie.genomique.eoulsan.util.ClassPathResourceLoader
 
reload() - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader
 
reload() - Method in interface fr.ens.biologie.genomique.eoulsan.util.ResourceLoader
Reload the list of available resources.
remove(EmergencyStopTask) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.EmergencyStopTasks
Remove an emergency task.
remove(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
remove(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
Remove the value according the key.
remove(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
remove(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
removeAllFiles() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Remove all the files of the working directory.
removedParameter(StepConfigurationContext, Parameter) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Throw a exception for removed parameters.
removedParameter(String, Parameter) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Throw a exception for removed parameters.
removeExperiment(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Remove the experiment.
removeFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
Remove a file of the analysis.
removeFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
 
removeFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Remove a file on the RServer.
removeFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
 
removeHadoopJobEmergencyStopTask(ClusterTaskScheduler, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask
Remove a cluster Job to the EmergencyStopTasks.
removeHadoopJobEmergencyStopTask(Job) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJobEmergencyStopTask
Remove an Hadoop Job to the EmergencyStopTasks.
removeInputFiles() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
 
removeInputFiles() - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor
Remove input files.
removeKey(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Remove a entry.
removeNamespace(String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter
Remove the namespace from the name of a variable.
removeObserver(StepObserver) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry
Remove a listener.
removeResourcePath(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader
Add a resource path.
removeSample(Sample) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment
Remove the sample.
removeSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
removeSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
removeSample(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Remove the sample.
removeStep(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepInstances
Remove a step instance.
removeThreadGroupLogger(ThreadGroup) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
Remove a logger for a thread group.
rename(DataFile, DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Rename a file.
rename(DataFile, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
rename(DataFile, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
 
renamedParameter(StepConfigurationContext, Parameter, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Show a message for deprecated parameters that has been renamed.
renamedParameter(StepConfigurationContext, Parameter, String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Show a message for deprecated parameters that has been renamed.
renamedParameter(String, Parameter, String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Show a message for deprecated parameters that has been renamed.
renameTo(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Rename the DataFile.
REP_TECH_GROUP_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
 
REP_TECH_GROUP_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
 
repack() - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJarRepackager
Repackage the jar application only if the repackaged file does not exist.
repack(File) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJarRepackager
Repackage the jar application.
replaceLocalPathBySymlinks(Design, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Replace the local paths in the design by paths to symbolic links in a directory.
replaceRtgNA(List<String>, List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Replace na values in RepTechGroup list to avoid pooling error.
REPORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor
 
REPORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor
 
REPORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor
 
REPORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MapperInputPreprocessor
 
Requirement - Interface in fr.ens.biologie.genomique.eoulsan.requirements
This interface define a requirement for an Eoulsan Step.
REQUIREMENT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
 
REQUIREMENT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
 
REQUIREMENT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
 
RequirementInstallerModule - Class in fr.ens.biologie.genomique.eoulsan.modules
This class allow to install a requirement.
RequirementInstallerModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
 
RequirementService - Class in fr.ens.biologie.genomique.eoulsan.requirements
This class define a service for requirements.
RequiresAllPreviousSteps - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations
This annotation is used to mark a step class that requires the all the previous step in the workflow file.
RequiresPreviousStep - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations
This annotation is used to mark a step class that requires the previous step in the workflow file.
reset() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
 
reset() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
 
resolveClass(ObjectStreamClass) - Method in class fr.ens.biologie.genomique.eoulsan.util.ClassLoaderObjectInputStream
 
ResourceLoader<S> - Interface in fr.ens.biologie.genomique.eoulsan.util
This interface define a resource loader.
resume() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MultiThreadTaskScheduler
 
resume() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.PausableThreadPoolExecutor
Resume the executor.
ReuseModuleInstance - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations
This annotation is used to mark a module class that can reuse a module instance for each task.
RExecutor - Interface in fr.ens.biologie.genomique.eoulsan.util.r
This interface define how to prepare, launch and retrieve data of a R analysis.
REXECUTOR_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor
 
REXECUTOR_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
 
REXECUTOR_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
 
RExecutorFactory - Class in fr.ens.biologie.genomique.eoulsan.util.r
This class define a factory to create RExecutor objects.
RExecutorFactory() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory
 
RExecutorFactory.Mode - Enum in fr.ens.biologie.genomique.eoulsan.util.r
Define a enum for the mode of RExecutor.
RmDupLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq
This class removes PCR duplicates from a SAM file.
RmDupLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule
 
RModuleCommonConfiguration - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana
This class define common methods used for the configuration of the step of the package.
RModuleCommonConfiguration() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration
 
ROOT_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
 
RSConnection - Class in fr.ens.biologie.genomique.eoulsan.util.r
This class define an enhanced connection to RServe.
RSConnection() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Default constructor.
RSConnection(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Public constructor.
RSCRIPT_EXECUTABLE - Static variable in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
 
RSERVE - fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory.Mode
 
RSERVE_SERVER_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration
 
RserveRequirement - Class in fr.ens.biologie.genomique.eoulsan.requirements
This class define a Rserve server requirement.
RserveRequirement() - Constructor for class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
 
RserveRExecutor - Class in fr.ens.biologie.genomique.eoulsan.util.r
This class define a RServe RExecutor.
RserveRExecutor(File, File, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
Public constructor.
RSingleCellExperimentCreatorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.singlecell
This class define a class that allow to create a SingleCellExperiment Bioconductor Object and save it as a RDS file.
RSingleCellExperimentCreatorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
 
run() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler.ProcessThreadOutput
 
run() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
 
run() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MonoThreadTaskScheduler
 
run() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MultiThreadTaskScheduler
 
run() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner
Run the task context.
run() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TokenManager
 
run() - Method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessThreadErrOutput
 
run(TaskContext, Data) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Run normalisation step
run(String[]) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp
This is the main driver for recursively copying directories across file systems.
runDEseq2(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2
Method to run DESeq2.
RUNNING - fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusValue
 
runRExecutor(TaskContext, Data) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Execute Rnw script.
runWithException(String[]) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp
This is the main driver for recursively copying directories across file systems.

S

SAM2BAMHadoopModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class define a module for converting SAM files into BAM.
SAM2BAMHadoopModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAM2BAMHadoopModule
 
SAM2BAMLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local
This class define a module for converting SAM files into BAM.
SAM2BAMLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAM2BAMLocalModule
 
SAM2FASTQLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local
This class define a module for converting SAM files into FASTQ.
SAM2FASTQLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAM2FASTQLocalModule
 
SAMFilterHadoopModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class define a filter alignment step in Hadoop mode.
SAMFilterHadoopModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterHadoopModule
 
SAMFilterLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local
This class define a Step for alignments filtering.
SAMFilterLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAMFilterLocalModule
 
SAMFilterMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class defines a mapper for alignment filtering.
SAMFilterMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterMapper
 
SAMFilterReducer - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class define a reducer for alignments filtering.
SAMFilterReducer() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterReducer
 
SAMHeaderHadoopUtils - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class contains methods and classes related to save and load SAM file header in Hadoop mappers and reducers.
SAMHeaderHadoopUtils() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils
 
SAMHeaderHadoopUtils.SAMHeaderWriter - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop
This class allow to save the SAM header read by a mapper.
SAMHeaderWriter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils.SAMHeaderWriter
Constructor.
SAMInputFormat - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
This class define an InputFormat for SAM files for the Hadoop MapReduce framework.
SAMInputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMInputFormat
 
SAMMerger - Class in fr.ens.biologie.genomique.eoulsan.splitermergers
This class define a merger class for SAM files.
SAMMerger() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMMerger
 
SAMOutputFormat - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
This class define a SAM output format.
SAMOutputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMOutputFormat
 
Sample - Interface in fr.ens.biologie.genomique.eoulsan.design
This interface defines a sample.
SAMPLE_ID_FIELD - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.Sample
Sample Id field.
SAMPLE_ID_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
 
SAMPLE_NAME_FIELD - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.Sample
Sample Name field.
SAMPLE_NAME_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
 
SAMPLE_NUMBER_FIELD - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.Sample
Sample Name field.
SAMPLE_NUMBER_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
 
SampleMetadata - Interface in fr.ens.biologie.genomique.eoulsan.design
This interface defines the sample metadata.
SAMRecordReader - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
This class define a RecordReader for SAM files for the Hadoop MapReduce framework.
SAMRecordReader(TaskAttemptContext) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
Public constructor.
SAMRecordWriter - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
This class define a RecordWriter for SAM files.
SAMRecordWriter(TaskAttemptContext, DataOutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordWriter
Public constructor.
SAMSequenceFile - Class in fr.ens.biologie.genomique.eoulsan.modules.fastqc
This class define a SequenceFile for SAM files.
SAMSequenceFile(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
Public constructor.
SAMSplitter - Class in fr.ens.biologie.genomique.eoulsan.splitermergers
This class define a splitter class for SAM files.
SAMSplitter() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMSplitter
 
SAVE_WORKFLOW_IMAGE_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Save workflow image.
saveConfigurationFiles() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
Save configuration files.
saveConfigurationFiles() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflow
 
saveDotFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.Workflow2Graphviz
Convert and save the workflow as a Graphviz file.
saveFinalResults(File) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.FinalExpressionFeaturesCreator
Save the final results.
saveFinalResults(OutputStream) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.FinalExpressionFeaturesCreator
Save the final results.
saveImageFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.Workflow2Graphviz
Convert and save the workflow as an image file.
saveMetaData(Data) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataMetadataStorage
Save metadata of a Data object.
saveSettings() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Save application options.
saveSettings(File) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Save application options.
SCHEDULER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.HTCondorTaskScheduler
 
SCHEDULER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.PBSProTaskScheduler
 
SCHEDULER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.SLURMTaskScheduler
 
SCHEDULER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TGCCTaskScheduler
 
SCHEDULER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TORQUETaskScheduler
 
SelectParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements
This class define a select tool element parameter.
SelectParameterToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement
Instantiates a new select tool element parameter.
SelectParameterToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement
Instantiates a new select tool element parameter.
sendMail(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
 
sendTokens(TaskContextImpl, TaskResultImpl) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner
Send tokens for a serialized task result.
SEP - Static variable in interface fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement
The Constant SEP.
separator - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFile
The separator char ('/') as a String.
separatorChar - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFile
The separator char ('/').
SERIAL_NUMBER_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
 
SerializableStopwatch - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
 
SerializableStopwatch() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.SerializableStopwatch
 
serialize(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Serialize the TaskContext object.
serialize(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
Serialize the TaskResult object.
serialize(File) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Serialize the TaskContext object.
serialize(File) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
Serialize the TaskResult object.
serialize(OutputStream) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Serialize the TaskContext object.
serialize(OutputStream) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
Serialize the TaskResult object.
serializeOutputData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Serialize output data.
serializeOutputData(File) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Serialize output data.
serializeOutputData(OutputStream) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
Serialize output data.
set(Data) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Set several field of the object from a Data object.
set(DataMetadata) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
The the entries of the metadata with the entries of another metadata object.
set(String, String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Set a metadata entry.
set(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
set(String, String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
Set the value according the key.
set(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
set(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
set(String, List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
set(String, List<String>) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
Set the value as a list according the key.
set(String, List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
set(String, List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
setAdditionalAnnotationFile(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
Set the additional annotation file.
setAdditionalAnnotationFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
 
setAdditionalAnnotationHypertextLinksPath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the additional annotation hypertext links path.
setAdditionalAnnotationStoragePath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the additional annotation storage path.
setArgv0Class(Class<?>) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
 
setAWSAccessKey(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the AWS access key.
setAWSSecretKey(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the AWS secret key.
setBuildContrast(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Set the buildContrast DEseq2 option.
setBuildContrast(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
setBypassPlatformChecking(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set if the platform checking must be avoided.
setClusterSchedulerName(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the name of the cluster scheduler.
setCommandArgs(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Override the commandArg() R function.
setCommandLine(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus
Set the context command line.
setCommandLine(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
setComment(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Set the comment.
setComparisons(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Set the comparisons DEseq2 option.
setComparisons(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
setCompression(CompressionType) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Set the compression
setCondition(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
Set the condition.
setCondition(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
 
setCondition(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Set the condition.
setCondition(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
setConf(Configuration) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp
 
setContextName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext
Set the context name.
setContextName(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
setContrast(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Set the contrast DEseq2 option.
setContrast(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
setContrastFile(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Set the contrastFile DEseq2 option.
setContrastFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
setCounters(Reporter, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus
Set the context counters.
setCounters(Reporter, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
setDataFile(Data, int, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils
Change the DataFile in a Data object
setDataFile(Data, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.DataUtils
Change the DataFile in a Data object
setDataFile(Data, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils
Change the DataFile in a Data object
setDataFiles(Data, List<DataFile>) - Static method in class fr.ens.biologie.genomique.eoulsan.core.DataUtils
Change the DataFiles in a Data object
setDataFiles(Data, List<DataFile>) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils
Change the DataFiles in a Data object
setDataFormatPath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the format path.
setDataFormatPaths(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the data format paths
setDataMetadata(Data, Data) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils
Set the metadata of a data object from the information of another data object.
setDataMetadata(Data, Collection<Data>) - Static method in class fr.ens.biologie.genomique.eoulsan.core.DataUtils
Set the metadata of a data object from the information of another data object.
setDataMetadata(Data, Collection<Data>) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils
Set the metadata of a data object from the information of another data object.
setDataMetaData(Data, Sample) - Static method in class fr.ens.biologie.genomique.eoulsan.core.DataUtils
Set the metadata of a data object from the information of a Sample object from a Design.
setDataMetaData(Data, Sample) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils
Set the metadata of a data object from the information of a Sample object from a Design.
setDataName(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Set the data name.
setDataPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Set the data directory path.
setDate(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Set the date.
setDebug(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the debug setting.
setDefaultClusterMemoryRequired(int) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the default memory required for the steps in cluster mode.
setDefaultFastqFormat(FastqFormat) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the Fastq format default value.
setDefaultLocale() - Static method in class fr.ens.biologie.genomique.eoulsan.Globals
Set the default Local of the application
setDescription(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus
Set the context description.
setDescription(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
setDescription(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Set the description.
setDesignFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Set the design file.
setDesignFile(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Set the designFile DEseq2 option.
setDesignFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
setDesignPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Set the design file path.
setDockerBackEnd(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the Docker URI.
setDockerBySingularityEnabled(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Enable Docker features using Singularity
setDockerConnectionURI(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the Docker URI.
setDockerMountNFSRoots(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set if when use Docker, NFS roots must been mounted instead of file paths.
setDockerSingularityStoragePath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the Docker singularity storage path.
setElementValue(ToolElement, Map<String, Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
Set the tool element value.
setExecutablesTempDirectory(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the temporary directory for executables.
setFastqFormat(FastqFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Set the FASTQ format of the data.
setFastqFormat(FastqFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Set the fastq format.
setFileIndex(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Set the file index.
setForceStepInstanceReuse(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner
Force the TaskRunner to reuse the original step instance when execute the task.
setFormat(DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Set the format.
setFormatter(Formatter) - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler
 
setGalaxyToolPath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the Galaxy tool path.
setGalaxyToolsPaths(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the Galaxy tools paths
setGenomeDescStoragePath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the genome description storage path.
setGenomeFile(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
Set the genome file.
setGenomeFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
 
setGenomeMapperIndexStoragePath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the genome index storage path.
setGenomeStoragePath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the genome storage path.
setGffFile(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
Set the gff file.
setGffFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
 
setGFFStoragePath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the GFF storage path.
setGtfFile(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
Set the gff file.
setGtfFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
 
setGTFStoragePath(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the GTF storage path.
setHadoopLogLevel(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the Hadoop log level.
setHadoopWorkingPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Set the local working path.
setHeaderMergerSortOrder(Configuration, SAMFileHeader.SortOrder) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
 
setImmutable() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Set the object immutable.
setInstallable(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
 
setJarFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Set the jar file.
setJobDescription(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Set job description.
setJobEnvironment(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Set job environment.
setJobPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Set the job path
setKeepRServeFiles(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set if save Rscripts is true
setLevel(Level) - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler
 
setLocalThreadsNumber(int) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the number of threads to use in local mode.
setLocalWorkingPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Set the local working path.
setLoggerName(String) - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
Set the logger name.
setMode(AbstractEoulsanRuntime.EoulsanExecMode) - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
Set the cluster mode.
setModel(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Set the model DEseq2 option.
setModel(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
setName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
Set the design name.
setName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment
Set the name of the experiment.
setName(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
setName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample
Set the sample name.
setName(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
setNote(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
Set the note.
setObfuscateDesign(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set if the design must be obfuscated
setObfuscateRemoveDesignInfo(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set if the replicate information must be removed from the design.
setOperator(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Set the operator.
setOptionnal(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
 
setOutputPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Set the output path
setOutputTreeType(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the output tree type.
setPairedEnd(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Set single-end/paired-end data type.
setPart(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Set the part number.
setPortName(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Set the port name.
setPrintStackTrace(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the print stack trace setting.
setProgress(double) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Progress
Set the progress of the processing.
setProgress(double) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
Set the progress of a step.
setProgress(double) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
setProgress(int, int, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Progress
Set the progress of the processing.
setProgress(int, int, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
Set the progress of a step.
setProgress(int, int, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
setProgressMessage(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Progress
Set the progress message.
setProgressMessage(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
 
setReads(List<String>) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Set the reads.
setReference(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
Set the reference.
setReference(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
 
setReference(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
setReference(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Set the reference option.
setReference(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
Set the reference.
setReference(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
 
setReference(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Set the reference.
setReference(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
setReference(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
setRepTechGroup(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
Set the ReptechGroup.
setRepTechGroup(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
 
setRepTechGroup(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Set the ReptechGroup.
setRepTechGroup(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
setResultMail(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the mail address for eoulsan results.
setRServeServerEnabled(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set if RServe is enabled.
setRServeServerName(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the RServe server name.
setSampleId(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Set the sample id related to the data
setSampleName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Set the sample name related to the data.
setSampleNumber(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Set the sample number related to the data.
setSampleNumber(int) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
Set the sample number related to the data
setSaveRscript(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set if save Rscripts is true
setSaveWorkflowImage(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set if an image of the workflow must be saved.
setSendResultMail(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set if an email must be sent at the end of the analysis.
setSerialNumber(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Set the serial number.
setSetting(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set a setting value.
setSetting(String, String, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set a setting value.
setSettings(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the values of the settings with another Settings object.
setSkip(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
Set the skip option.
setSkip(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
setSMTPHost(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the SMTP server host.
setStepId(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming
Set the step id.
setTaskDone(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
Set task done.
setTaskPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Set the task path
setTaskProgress(int, String, double) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
Set the progress of a task.
setTaskProgress(int, String, int, int, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
Set the progress of a task.
setTaskRunning(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
Set task running.
setTaskSubmitted(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
Set task submitted.
setTempDirectory(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the temporary directory.
setTemporaryPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Set the temporary directory path.
Settings - Class in fr.ens.biologie.genomique.eoulsan
This class define a settings class.
setUIName(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the UI name.
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.HadoopCompatibleTaskScheduler.HadoopCompatibleMapper
 
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionMapper
 
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentMapper
 
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DataFileDistCp.DistCpMapper
 
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionMapper
 
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionSAMOutputMapper
 
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterMapper
 
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperMapper
 
setup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterMapper
 
setup(Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionReducer
 
setup(Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentReducer
 
setup(Reducer.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterReducer
 
setUseOldEoulsanResultFormat(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set if Eoulsan result files must be written using the old format.
setUseStandardExternalModules(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set if standard external modules must be used.
setUUID(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Set the UUID.
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement
 
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
 
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement
 
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
 
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement
 
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.IntegerParameterToolElement
 
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement
 
setValue(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement
 
setValue(String) - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement
Sets the value.
setValues(Map<String, Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
Set the values.
setWorkflowFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext
Set the workflow file.
setWorkflowPathname(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
Set the workflow file path.
setWorking(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
setZooKeeperConnectString(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the ZooKeeper connect string.
setZooKeeperDefaultPort(int) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the ZooKeeper default port.
setZooKeeperSessionTimeout(int) - Method in class fr.ens.biologie.genomique.eoulsan.Settings
Set the ZooKeeper session timeout.
sh(List<String>) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
Execute a command.
sh(List<String>, File) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
Execute a command.
ShellModule - Class in fr.ens.biologie.genomique.eoulsan.modules
This class define a module that execute a shell command.
ShellModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
 
showAndLogErrorMessage(String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
Show and log an error message.
showDesign(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils
Show a design
showErrorMessageAndExit(String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
Show a message and then exit.
showInfo(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractInfoAction
Show the information on stdout
showInfo(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.actions.FormatsAction
 
showInfo(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.actions.InfoAction
Show the information on stdout
showInfo(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ModulesAction
 
showMessageAndExit(String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
Show a message and then exit.
SimpleInputPort - Class in fr.ens.biologie.genomique.eoulsan.core
This class define an input port of a step.
SimpleInputPort(String, boolean, DataFormat, EnumSet<CompressionType>, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPort
Constructor.
SimpleInputPort(String, DataFormat, EnumSet<CompressionType>, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPort
Constructor.
SimpleInputPorts - Class in fr.ens.biologie.genomique.eoulsan.core
This class define a class that handles a set of input ports.
SimpleOutputPort - Class in fr.ens.biologie.genomique.eoulsan.core
This class define an output port of a step.
SimpleOutputPort(String, boolean, DataFormat, CompressionType) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPort
Constructor.
SimpleOutputPort(String, DataFormat, CompressionType) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPort
Constructor.
SimpleOutputPorts - Class in fr.ens.biologie.genomique.eoulsan.core
This class define a class that contains several output ports.
SINGLE_CELL_EXPERMIMENT_RDS - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
R single cell experiment.
singleInputPort(DataFormat) - Static method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Convenient method to create the ports with only one port.
singleInputPort(String, DataFormat) - Static method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder
Convenient method to create the ports with only one port.
singleOutputPort(DataFormat) - Static method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder
Convenient method to create the ports with only one port.
singleOutputPort(String, DataFormat) - Static method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder
Convenient method to create the ports with only one port.
size() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
 
size() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports
Get the number of ports in the object.
size() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
size() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data
Get the size of the data.
size() - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
size() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
Get the number of metadata.
size() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
 
size() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
skip(long) - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
 
SKIP_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
 
SLURMTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This class define a SLURM cluster scheduler using a Bpipe script.
SLURMTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.SLURMTaskScheduler
Constructor.
softwareInfos(Main) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with Eoulsan software informations.
Splice2BEDModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local
This class define a module for converting SAM files into BED.
Splice2BEDModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.Splice2BEDModule
 
split(DataFile, Iterator<DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMSplitter
 
split(DataFile, Iterator<DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionSplitter
 
split(DataFile, Iterator<DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqSplitter
 
split(DataFile, Iterator<DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMSplitter
 
split(DataFile, Iterator<DataFile>) - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Splitter
Split data.
splitByChromosomes(DataFile, Iterator<DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMSplitter
Split BAM file by chromosomes.
splitByChromosomes(DataFile, Iterator<DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMSplitter
Split SAM file by chromosomes.
Splitter - Interface in fr.ens.biologie.genomique.eoulsan.splitermergers
This interface define a splitter.
SplitterModule - Class in fr.ens.biologie.genomique.eoulsan.modules
This class define a generic splitter module.
SplitterModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
 
STANDARD - fr.ens.biologie.genomique.eoulsan.core.ParallelizationMode
 
STANDARD_EXTERNAL_MODULES_ENABLED_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Enable standard external modules.
STANDARD_EXTERNAL_MODULES_ENABLED_KEY - Static variable in class fr.ens.biologie.genomique.eoulsan.Settings
 
STANDARD_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
 
STAR_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
STAR index data format.
STARIndexGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators
This class define a module that generate a STAR mapper index.
STARIndexGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
 
start() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
start() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
 
start() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
 
start() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MonoThreadTaskScheduler
 
start() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MultiThreadTaskScheduler
 
start() - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler
Start the scheduler.
start() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.SerializableStopwatch
 
statusJob(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
 
statusJob(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler
Get the status of a job.
StatusResult(ClusterTaskScheduler.StatusValue) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusResult
Constructor.
StatusResult(ClusterTaskScheduler.StatusValue, int) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusResult
Constructor.
STD_OUTPUT_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Default standard output state.
Step - Interface in fr.ens.biologie.genomique.eoulsan.core
This interface define a step of the workflow.
STEP_LOG_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Step log extension.
STEP_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
 
STEP_OUTPUT_DIRECTORY_SUFFIX - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Step output directory suffix.
STEP_RESULT_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Step result extension.
STEP_RESULT_OLD_FORMAT_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Old step result format extension.
Step.DiscardOutput - Enum in fr.ens.biologie.genomique.eoulsan.core
This enum define the value of the discard output attribute of the step tag in the Eoulsan workflow file.
Step.StepState - Enum in fr.ens.biologie.genomique.eoulsan.core
This enum define the states of the steps.
Step.StepType - Enum in fr.ens.biologie.genomique.eoulsan.core
This enum define the type of step.
StepConfigurationContext - Interface in fr.ens.biologie.genomique.eoulsan.core
 
StepConfigurationContextImpl - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a concrete implementation of the configuration context of a step.
stepId - Variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser.StepOutputPort
 
StepInstances - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class store module instances and avoid storing this instance in Step objects that are serialized.
StepObserver - Interface in fr.ens.biologie.genomique.eoulsan.core.workflow
This interface define workflow step events
StepObserverRegistry - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class allow to relay workflow step events to other observers.
StepOutputDataFile - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define an output file of workflow set.
StepOutputDataFile(StepOutputPort, Sample) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
Constructor.
StepOutputDataFile(StepOutputPort, Sample, int) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
Constructor.
StepOutputPort(String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser.StepOutputPort
 
StepResult - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a step result.
StepResult(AbstractStep) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Constructor.
StepStateDependencies - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class allow to store the step state and its dependencies.
StepStateDependencies(AbstractStep) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies
Constructor.
stepStateEvent(StepStateEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
Listen StepState events.
stepStateEvent(StepStateEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry
Handle step state change events.
stepStateEvent(StepStateEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies
Listen StepState events.
StepStatus - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a step status.
StepStatus(AbstractStep) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus
 
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
 
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler
 
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask
 
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
 
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.HadoopCompatibleTaskScheduler
 
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MultiThreadTaskScheduler
 
stop() - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler
Stop the scheduler.
stop() - Method in interface fr.ens.biologie.genomique.eoulsan.core.workflow.EmergencyStopTask
Execute the stop task.
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.EmergencyStopTasks
Stop all the tasks.
stop() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.SerializableStopwatch
 
stop() - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJobEmergencyStopTask
 
stopJob(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
 
stopJob(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler
Stop a job.
StorageDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This abstract class define a storage protocol.
StorageDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
 
storageInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with storage informations.
submit(Step, TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
submit(Step, TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
 
submit(Step, TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler
 
submit(Step, TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
 
submit(Step, TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.HadoopCompatibleTaskScheduler
 
submit(Step, TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MonoThreadTaskScheduler
 
submit(Step, TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.MultiThreadTaskScheduler
 
submit(Step, TaskContextImpl) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler
Submit a context to execute.
submit(Step, Set<TaskContextImpl>) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
submit(Step, Set<TaskContextImpl>) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
 
submit(Step, Set<TaskContextImpl>) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
 
submit(Step, Set<TaskContextImpl>) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler
Submit contexts to execute.
submit(Runnable, T, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.PausableThreadPoolExecutor
Submit a task.
submitAndWaitForJob(Job, String, int, TaskStatus, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.MapReduceUtils
Wait the completion of a job.
submitJob(String, List<String>, File, int, int, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
 
submitJob(String, List<String>, File, int, int, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler
Submit a job.
SUCCESS - fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput
 
SuffixPathFilter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils.SuffixPathFilter
Public constructor.
SuffixPathFilter(String, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils.SuffixPathFilter
Public constructor.
symlink(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Create a symbolic link that target is the current file.
symlink(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Create a symbolic link that target is the current file.
symlink(DataFile, DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol
Create a symbolic link.
symlink(DataFile, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
 
symlinkOrCopy(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.data.DataFiles
Create a symbolic link if the input and output use the same protocol and if symbolic links are supported by the protocol.
symlinkOrCopy(DataFile, DataFile, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.data.DataFiles
Create a symbolic link if the input and output use the same protocol and if symbolic links are supported by the protocol.
symlinkOrCopy(DataPath) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
sysInfoLog() - Method in class fr.ens.biologie.genomique.eoulsan.Main
Log system information.
sysInfoLog() - Method in class fr.ens.biologie.genomique.eoulsan.MainHadoop
 
system(String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
Execute a command.
SYSTEM_CHARSET - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets
The system default charset.
SYSTEM_FILE_ENCODING - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets
The system default charset.
systemInfos() - Static method in class fr.ens.biologie.genomique.eoulsan.Infos
Return a list with system informations.

T

TAG_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement
The Constant TAG_NAME.
TARGET_CREATION - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
 
TASK_CONTEXT_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Task context extension.
TASK_DATA_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Task output data extension.
TASK_DONE_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Task done extension.
TASK_JOB_ID - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Task jobb id extension.
TASK_LOG_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Task done extension.
TASK_RESULT_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Task result extension.
TASK_STDERR_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Task stderr extension.
TASK_STDOUT_EXTENSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Task stdout extension.
TaskContext - Interface in fr.ens.biologie.genomique.eoulsan.core
This interface define the context of a step.
TaskContextImpl - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a task context.
TaskResult - Interface in fr.ens.biologie.genomique.eoulsan.core
This class define the result of a step.
TaskResultImpl - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a result for a task context.
TaskResultImpl(TaskContextImpl, Date, Date, long, Throwable, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
 
TaskRunner - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class allow to run a task context.
TaskRunner(TaskContextImpl) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner
Constructor.
TaskRunner(TaskContextImpl, StepStatus) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner
Constructor.
TaskScheduler - Interface in fr.ens.biologie.genomique.eoulsan.core.schedulers
This interface define a task scheduler.
TaskSchedulerFactory - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers
This class define a factory for TaskScheduler that can create only one instance.
TaskSerializationUtils - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class contains utility methods for serialization, deserialization and execution of Task objects.
TaskSerializationUtils() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskSerializationUtils
 
TaskStatus - Interface in fr.ens.biologie.genomique.eoulsan.core
This interface define a step status.
TaskStatusImpl - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a task status.
TechnicalReplicateMergerModule - Class in fr.ens.biologie.genomique.eoulsan.modules
This class define a merger module for technical replicates.
TechnicalReplicateMergerModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule
 
TEMP_PREFIX - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
The prefix for temporary files.
Terminal - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations
This annotation is used to mark a step class that is a terminal step.
TERMINAL_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
 
TerminalModule - Class in fr.ens.biologie.genomique.eoulsan.modules
This class define a terminal task that do nothing.
TerminalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.TerminalModule
 
TextParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements
This class define a text tool element parameter.
TextParameterToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement
Instantiates a new text tool element parameter.
TextParameterToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement
Instantiates a new text tool element parameter.
TGCCTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This class define a TGCC cluster scheduler.
TGCCTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TGCCTaskScheduler
 
throwExitCodeException(int, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
Throw an IOException if the exit code of a process is not equals to 0.
Ticket - Class in fr.ens.biologie.genomique.eoulsan.util.locker
This class define a ticket for the TicketLocker.
Ticket() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
Ticket(int, long, long, long, String, long, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
Ticket(Ticket) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
Ticket(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
TicketLocker - Class in fr.ens.biologie.genomique.eoulsan.util.locker
This class define a global locker using RMI messaging.
TicketLocker(String, int) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.TicketLocker
Public constructor.
TicketLocker(String, int, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.TicketLocker
Public constructor.
TicketScheduler - Interface in fr.ens.biologie.genomique.eoulsan.util.locker
Define the rmi interface for the TicketSchedulerServer.
TicketSchedulerServer - Class in fr.ens.biologie.genomique.eoulsan.util.locker
This class define a server for the scheduler.
toAbsoluteDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Convert the the DataFile to a absolute DataFile.
toDESeq2Value() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType
Convert the enum name into DESeq2 value.
toDESeq2Value() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.SizeFactorsType
Convert the enum name into DESeq2 value.
toDESeq2Value() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.StatisticTest
 
toEoulsanLogV1() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Get a representation of the result in the old Eoulsan format.
toFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Convert the DataFile object to File object if the underlying protocol allow it.
toFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
toJSON() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Convert the object to JSON
tokenEvent(Token) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TokenManager
 
TokenManager - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a token manager for a step.
TokenManagerRegistry - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class store all the TokenManager instances.
ToolElement - Interface in fr.ens.biologie.genomique.eoulsan.galaxytools.elements
The ToolElement interface.
ToolElementFactory - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements
This class define a factory for ToolElement objects.
ToolElementFactory() - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElementFactory
 
ToolExecutor - Class in fr.ens.biologie.genomique.eoulsan.galaxytools
The class define an executor on tool set in XML file.
ToolExecutor(TaskContext, ToolInfo, String, Set<File>) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutor
Constructor a new galaxy tool executor.
ToolExecutorResult - Class in fr.ens.biologie.genomique.eoulsan.galaxytools
The class define a result on execution tool.
ToolExecutorResult(List<String>, int) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult
Public constructor, command line can not be null or empty
ToolExecutorResult(List<String>, Throwable) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult
Public constructor, command line can not be null or empty
ToolInfo - Class in fr.ens.biologie.genomique.eoulsan.galaxytools
The class define a tool data which contains all data extracted from XML file.
toPath() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Convert the DataFile object to Path object if the underlying protocol allow it.
toRealDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Convert the the DataFile to a DataFile where all the indirection has been solved.
TORQUETaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters
This class define a TORQUE cluster scheduler using a Bpipe script.
TORQUETaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TORQUETaskScheduler
Constructor.
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPort
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPort
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIEvent
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.IntegerParameterToolElement
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.GenericExecutorInterpreter
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo
 
toString() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
toString() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.Settings
 
toString() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
TOTAL_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
TOTAL_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
toUri() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
Convert the DataFile object to an URI.
toValidName(String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Naming
Convert a string to a valid name string that can be used for step id or data name.
toXML() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel
Convert the object in XML.
TrackHubModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq
This class construct TrackHub for genome browser visualization.
TrackHubModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
 
tryLock(long, TimeUnit) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock
 
TYPE - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement
The Constant TYPE.
TYPE - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
The Constant TYPE.
TYPE - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement
The Constant TYPE.
TYPE - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement
The Constant TYPE.
TYPE - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.IntegerParameterToolElement
The Constant TYPE.
TYPE - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.SelectParameterToolElement
The Constant TYPE.
TYPE - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.TextParameterToolElement
The Constant TYPE.

U

UI - Interface in fr.ens.biologie.genomique.eoulsan.ui
This interface define how UI is informed of The workflow changes.
UI_NAME_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Default UI name.
UIEvent - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define an abstract UIEvent
UIEvent() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.UIEvent
 
UIService - Class in fr.ens.biologie.genomique.eoulsan.ui
This class define a service to retrieve a UI.
uiStepEvent(UIStepEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry
Handle UI step events.
UIStepEvent - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a UI step event.
uiTaskEvent(UITaskEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry
Handle UI task events.
UITaskEvent - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a UI task event.
UITaskEvent(Step, UITaskEvent.TaskStatusMessage, int) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.UITaskEvent
Constructor.
uiWorkflowEvent(UIWorkflowEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry
Handle UI workflow events.
UIWorkflowEvent - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a UI workflow event.
UIWorkflowEvent(boolean, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.UIWorkflowEvent
Constructor.
uk.ac.babraham.FastQC.Report - package uk.ac.babraham.FastQC.Report
 
UNKNOWN - fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusValue
 
unknownParameter(StepConfigurationContext, Parameter) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Throw a exception for unknown parameters.
unknownParameter(String, Parameter) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules
Throw a exception for unknown parameters.
unlock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock
 
unlock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLocker
 
unlock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ExecFileLock
 
unlock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ExecLock
 
unlock() - Method in interface fr.ens.biologie.genomique.eoulsan.util.locker.Locker
Unlock the resource.
unlock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.TicketLocker
 
unlock() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ZooKeeperLocker
 
UNMAP_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
 
UNMAP_READS_FASTA - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats
Unmap reads results data format.
UNMAPPED_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
UnmodifiableData - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define an unmodifiable data
unmodifiableDesign(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignFactory
Create an unmodifiable wrapper around an existing design.
UnmodifiableExperiment - Class in fr.ens.biologie.genomique.eoulsan.design
 
UnmodifiableExperiment(Experiment) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
 
UnmodifiableExperimentMetadata - Class in fr.ens.biologie.genomique.eoulsan.design
 
UnmodifiableExperimentSampleMetadata - Class in fr.ens.biologie.genomique.eoulsan.design
 
UnmodifiableExperimentSampleMetadata(ExperimentSampleMetadata) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
 
unregister(Object) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowEventBus
Unregister an listener object.
UNUSED_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
unZipPathToLocalFile(Path, File, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Unzip a zip file on local file system.
unZipPathToLocalFile(Path, File, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils
Unzip a zip file on local file system.
updateLastActiveTime() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
 
UploadModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload
This class define a abstract module class for files uploading.
UploadModule(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
Public constructor.
URLDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols
This class define an abstract class for DataProtocols based on the URL class.
URLDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
 
USE_BUNDLED_BINARIES_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
 
USE_OLD_EOULSAN_RESULT_FORMAT_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Write results using old Eoulsan format.
USED_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
 
UTF8_CHARSET - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets
UTF-8 charset.
UTF8_FILE_ENCODING - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets
UTF-8 file encoding.
Utils - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli
 
Utils() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
 
UUID_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
 

V

valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.core.ParallelizationMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusValue
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepState
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.SizeFactorsType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.StatisticTest
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory.Mode
Returns the enum constant of this type with the specified name.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.core.ParallelizationMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusValue
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepState
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.SizeFactorsType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.StatisticTest
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory.Mode
Returns an array containing the constants of this enum type, in the order they are declared.
VAR_CMD_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter
The Constant VAR_CMD_NAME.
VERSION_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Version constant name.

W

waitEndOfTasks(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
 
waitEndOfTasks(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
 
waitEndOfTasks(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
 
waitEndOfTasks(Step) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler
Wait the end of the task contexts.
waitForCompletion(Job, int) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.MapReduceUtils
Wait for job completion.
WAITING - fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusValue
 
WAITING - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
 
waitRandom(int) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
Wait a random number of milliseconds.
waitUntilExecutableRunning(String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils
Wait the end of the execution of all the instance of an executable.
WALD - fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.StatisticTest
 
WEBSITE_URL - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
Application Website url.
WELCOME_MSG - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
The welcome message.
WORK_FILENAME_PROPERTY - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
 
Workflow - Interface in fr.ens.biologie.genomique.eoulsan.core
This interface define a Workflow.
WORKFLOW_COPY_FILENAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
 
WORKFLOW_FILE_PATH_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser
Parameters file path constant name.
Workflow2Graphviz - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
Convert a Workflow to Graphviz
Workflow2Graphviz(AbstractWorkflow, DataFile, DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.Workflow2Graphviz
Public constructor.
WorkflowContext - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define the context implementation.
WorkflowDataUtils - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define an utility on data object.
WorkflowEventBus - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class define a single for the event bus.
WorkflowFileNaming - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
This class contains methods to create workflow data file names.
WORKING - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
 
write(byte[]) - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream
 
write(byte[]) - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterOutputStream
 
write(byte[], int, int) - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream
 
write(byte[], int, int) - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterOutputStream
 
write(int) - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream
 
write(int) - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterOutputStream
 
write(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Write the result.
write(Design) - Method in interface fr.ens.biologie.genomique.eoulsan.design.io.DesignWriter
 
write(Design) - Method in class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter
 
write(Design) - Method in class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter
 
write(OutputStream, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult
Write the result.
write(Text, LongWritable) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.ExpressionRecordWriter
 
write(Text, Text) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordWriter
 
write(Text, Text) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordWriter
 
writeIfHeaderLine(JobContext, String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils.SAMHeaderWriter
Write the line to the SAM header file if the line is a SAM header.
writeLog(File, long, String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
Write log data.
writeLog(OutputStream, long, String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common
Write log data.
writerFile(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
 
writerFile(String, String) - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor
Write a file.
writerFile(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
 
writeStringAsFile(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection
Write a file to the RServer.

X

XMLDataFormat - Class in fr.ens.biologie.genomique.eoulsan.data
This class define a DataFormat from an XML file.
XMLDataFormat(InputStream, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
Public constructor.

Z

ZOOKEEPER_DEFAULT_PORT_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
ZooKeeper default port.
ZOOKEEPER_SESSION_TIMEOUT_DEFAULT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals
ZooKeeper default session timeout.
ZooKeeperLocker - Class in fr.ens.biologie.genomique.eoulsan.util.locker
This class implements a locker using Zookeeper.
ZooKeeperLocker(String, int, String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.ZooKeeperLocker
Public constructor.
ZooKeeperLocker(String, int, String, String, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.ZooKeeperLocker
Public constructor.
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