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Eoulsan 2.4 API

This document is the API of Eoulsan.

See: Description

Packages 
Package Description
fr.ens.biologie.genomique.eoulsan
Root package of Eoulsan.
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
This package define the annotations on Eoulsan classes plug-ins.
fr.ens.biologie.genomique.eoulsan.bio
This package define an object model to handle NGS biological data.
fr.ens.biologie.genomique.eoulsan.bio.alignmentsfilters
This package contains and define alignments filters.
fr.ens.biologie.genomique.eoulsan.bio.expressioncounters  
fr.ens.biologie.genomique.eoulsan.bio.io
This package contains I/O classes for reading and writing objects of the fr.ens.biologie.genomique.eoulsan.bio.alignmentsfilters 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.bio.readsfilters
This package contains and define reads filters.
fr.ens.biologie.genomique.eoulsan.bio.readsmappers
This package contains and define reads mappers.
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.data.protocols
This package contains class for protocols used by the DataFile classes.
fr.ens.biologie.genomique.eoulsan.data.storages
This package contains and define data storages.
fr.ens.biologie.genomique.eoulsan.design
This package contains classes to handle experimental designs.
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
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.galaxytools.executorinterpreters
This package contain classes related to the Galaxy tool executor interpreters.
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.io.comparators
This package contains classes for compare files.
fr.ens.biologie.genomique.eoulsan.it
This package contains classes for integrative tests.
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
This package contain classes related data management (e.g.
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 Amazon S3.
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.translators
This package contain classes related to translators.
fr.ens.biologie.genomique.eoulsan.translators.io
This package contain classes related to translators I/O.
fr.ens.biologie.genomique.eoulsan.ui
This package contains Eoulsan user interface classes.
fr.ens.biologie.genomique.eoulsan.util
This package contain utility classes.
fr.ens.biologie.genomique.eoulsan.util.cloud
This package contains utility classes for cloud computing.
fr.ens.biologie.genomique.eoulsan.util.hadoop
This package contains utility classes for hadoopS.
fr.ens.biologie.genomique.eoulsan.util.locker
This package contain an advanced multi JVM lock system.
fr.ens.biologie.genomique.eoulsan.util.process
This package contain utility classes for processes usage.
fr.ens.biologie.genomique.eoulsan.util.r
This package contain utility classes for R usage.
This document is the API of Eoulsan. You can find more information about how to use this API on the Eoulsan developer wiki and on the Eoulsan website.
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