Eoulsan 2.7 API
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.
Packages
Package
Description
Root package of Eoulsan.
This package contains all the commands (actions) available through the Eoulsan command line.
This package define the annotations on Eoulsan classes plug-ins.
This package contains I/O classes for reading objects of the
fr.ens.biologie.genomique.eoulsan.bio.alignmentsfilters package from Hadoop.This package contains and define checkers of DataFormat.
This package contains Eoulsan workflow core class.
This package contains classes for schedulers.
This package contains classes for cluster schedulers.
This package contains Eoulsan workflow dedicated classes.
This package contains classes for data files, data types and data formats.
This package contains class for protocols used by the
DataFile classes.This package contains and define data storages.
This package contains classes to handle experimental designs.
This package contains I/O classes to read and write design files.
This package contain classes related to read tool xml file from galaxy.
This package contain classes related to parameter extractions from XML Galaxy tool xml files.
This package contain classes related to the Galaxy tool executor interpreters.
This package contains general I/O classes for Eoulsan (not dedicated to
fr.ens.biologie.genomique.eoulsan.bio package).This package define the steps for the Eoulsan workflow.
This packages contains the ChIP-Seq modules.
This packages contains the peak-calling modules.
This packages contains all the quality check modules for ChIP-Seq.
This package contain all the classes related to the differential analysis step.
This package contain all the classes related to the expression step.
This package contain all the classes related to the expression step in hadoop mode.
This package contain all the classes related to the expression step in local mode.
This package contain all the classes related to FastQC.
This package contain generator steps.
This package contain all the classes related to the mapping (reads filtering, mapping and
alignments filtering) step.
This package contain all the classes related to the mapping (reads filtering, mapping and
alignments filtering) step in hadoop mode.
This package contain all the classes related to the mapping (reads filtering, mapping and
alignments filtering) step in local mode.
This package contain classes related data management (e.g.
This package contain classes related data management in Hadoop mode.
This package contain classes related to upload data to HDFS and Cloud.
This package contains requirement classes for Eoulsan.
This package contains splitter and merger used when running Eoulsan on a standard cluster to get
more parallelization efficiency.
This package contains Eoulsan user interface classes.
This package contain utility classes.
This package contains utility classes for hadoopS.
This package contain an advanced multi JVM lock system.
This package contain utility classes for R usage.