Uses of Package
fr.ens.biologie.genomique.eoulsan.core
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Packages that use fr.ens.biologie.genomique.eoulsan.core Package Description fr.ens.biologie.genomique.eoulsan.annotations This package define the annotations on Eoulsan classes plug-ins.fr.ens.biologie.genomique.eoulsan.checkers This package contains and define checkers of DataFormat.fr.ens.biologie.genomique.eoulsan.core This package contains Eoulsan workflow core class.fr.ens.biologie.genomique.eoulsan.core.schedulers This package contains classes for schedulers.fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters This package contains classes for cluster schedulers.fr.ens.biologie.genomique.eoulsan.core.workflow This package contains Eoulsan workflow dedicated classes.fr.ens.biologie.genomique.eoulsan.data This package contains classes for data files, data types and data formats.fr.ens.biologie.genomique.eoulsan.galaxytools This package contain classes related to read tool xml file from galaxy.fr.ens.biologie.genomique.eoulsan.galaxytools.elements This package contain classes related to parameter extractions from XML Galaxy tool xml files.fr.ens.biologie.genomique.eoulsan.modules This package define the steps for the Eoulsan workflow.fr.ens.biologie.genomique.eoulsan.modules.chipseq This packages contains the ChIP-Seq modules.fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling This packages contains the peak-calling modules.fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc This packages contains all the quality check modules for ChIP-Seq.fr.ens.biologie.genomique.eoulsan.modules.diffana This package contain all the classes related to the differential analysis step.fr.ens.biologie.genomique.eoulsan.modules.expression This package contain all the classes related to the expression step.fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop This package contain all the classes related to the expression step in hadoop mode.fr.ens.biologie.genomique.eoulsan.modules.expression.local This package contain all the classes related to the expression step in local mode.fr.ens.biologie.genomique.eoulsan.modules.fastqc This package contain all the classes related to FastQC.fr.ens.biologie.genomique.eoulsan.modules.generators This package contain generator steps.fr.ens.biologie.genomique.eoulsan.modules.mapping This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step.fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in hadoop mode.fr.ens.biologie.genomique.eoulsan.modules.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.hadoop This package contain classes related data management in Hadoop mode.fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload This package contain classes related to upload data to HDFS and Cloud.fr.ens.biologie.genomique.eoulsan.modules.multiqc fr.ens.biologie.genomique.eoulsan.modules.singlecell fr.ens.biologie.genomique.eoulsan.requirements This package contains requirement classes for Eoulsan.fr.ens.biologie.genomique.eoulsan.splitermergers This package contains splitter and merger used when running Eoulsan on a standard cluster to get more parallelization efficiency.fr.ens.biologie.genomique.eoulsan.ui This package contains Eoulsan user interface classes.fr.ens.biologie.genomique.eoulsan.util.hadoop This package contains utility classes for hadoopS. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.annotations Class Description Module This interface define a Module. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.checkers Class Description Parameter This class define a parameter. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.core Class Description AbstractPort Abstract class that define a port.AbstractPorts This class define a basic implementation of a Ports class.FileNaming This class contains methods to create workflow data file names.InputPort This interface define an input port of a step.InputPorts This interface define a group of input ports.InputPortsBuilder This class allow to easily create input ports for a step.OutputPort This interface define an output port of a step.OutputPorts This interface define a group of output ports.OutputPortsBuilder This class allow to easily create input ports for a step.ParallelizationMode This enum define the parallelization modes of a step.Parameter This class define a parameter.Port This interface define a port of a step.Ports This interface define a group of ports.Progress This interface allow to set the progress of a task.Step This interface define a step of the workflow.Step.DiscardOutput This enum define the value of the discard output attribute of the step tag in the Eoulsan workflow file.Step.StepState This enum define the states of the steps.Step.StepType This enum define the type of step.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status.Workflow This interface define a Workflow. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.core.schedulers Class Description Step This interface define a step of the workflow. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters Class Description Step This interface define a step of the workflow. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.core.workflow Class Description FileNaming This class contains methods to create workflow data file names.InputPort This interface define an input port of a step.InputPorts This interface define a group of input ports.Module This interface define a Module.OutputPorts This interface define a group of output ports.ParallelizationMode This enum define the parallelization modes of a step.Parameter This class define a parameter.Progress This interface allow to set the progress of a task.Step This interface define a step of the workflow.Step.DiscardOutput This enum define the value of the discard output attribute of the step tag in the Eoulsan workflow file.Step.StepState This enum define the states of the steps.Step.StepType This enum define the type of step.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status.Workflow This interface define a Workflow. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.data Class Description Module This interface define a Module. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.galaxytools Class Description Parameter This class define a parameter.TaskContext This interface define the context of a step. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.galaxytools.elements Class Description Parameter This class define a parameter. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules Class Description InputPorts This interface define a group of input ports.Module This interface define a Module.OutputPorts This interface define a group of output ports.ParallelizationMode This enum define the parallelization modes of a step.Parameter This class define a parameter.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.chipseq Class Description InputPorts This interface define a group of input ports.Module This interface define a Module.OutputPorts This interface define a group of output ports.Parameter This class define a parameter.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling Class Description InputPorts This interface define a group of input ports.Module This interface define a Module.OutputPorts This interface define a group of output ports.Parameter This class define a parameter.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc Class Description InputPorts This interface define a group of input ports.Module This interface define a Module.Parameter This class define a parameter.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.diffana Class Description InputPorts This interface define a group of input ports.Module This interface define a Module.OutputPorts This interface define a group of output ports.ParallelizationMode This enum define the parallelization modes of a step.Parameter This class define a parameter.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.expression Class Description InputPorts This interface define a group of input ports.Module This interface define a Module.OutputPorts This interface define a group of output ports.ParallelizationMode This enum define the parallelization modes of a step.Parameter This class define a parameter.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop Class Description InputPorts This interface define a group of input ports.Module This interface define a Module.Parameter This class define a parameter.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.expression.local Class Description Module This interface define a Module.TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.fastqc Class Description InputPorts This interface define a group of input ports.Module This interface define a Module.OutputPorts This interface define a group of output ports.Parameter This class define a parameter.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.generators Class Description InputPorts This interface define a group of input ports.Module This interface define a Module.OutputPorts This interface define a group of output ports.Parameter This class define a parameter.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.mapping Class Description InputPorts This interface define a group of input ports.Module This interface define a Module.OutputPorts This interface define a group of output ports.Parameter This class define a parameter.StepConfigurationContext -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop Class Description InputPorts This interface define a group of input ports.Module This interface define a Module.Parameter This class define a parameter.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.mapping.local Class Description InputPorts This interface define a group of input ports.Module This interface define a Module.OutputPorts This interface define a group of output ports.ParallelizationMode This enum define the parallelization modes of a step.TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop Class Description Module This interface define a Module.Parameter This class define a parameter.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload Class Description Module This interface define a Module.Parameter This class define a parameter.Step This interface define a step of the workflow.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.multiqc Class Description InputPorts This interface define a group of input ports.Module This interface define a Module.OutputPorts This interface define a group of output ports.Parameter This class define a parameter.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.modules.singlecell Class Description InputPorts This interface define a group of input ports.Module This interface define a Module.OutputPorts This interface define a group of output ports.Parameter This class define a parameter.StepConfigurationContext TaskContext This interface define the context of a step.TaskResult This class define the result of a step.TaskStatus This interface define a step status. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.requirements Class Description Parameter This class define a parameter.Progress This interface allow to set the progress of a task. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.splitermergers Class Description Parameter This class define a parameter. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.ui Class Description Step This interface define a step of the workflow.Step.StepState This enum define the states of the steps.Workflow This interface define a Workflow. -
Classes in fr.ens.biologie.genomique.eoulsan.core used by fr.ens.biologie.genomique.eoulsan.util.hadoop Class Description TaskStatus This interface define a step status.