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.
| 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.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 |
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.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.hadoop.hadoopbamcli | |
| 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 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 |
This package contain utility classes.
|
| fr.ens.biologie.genomique.eoulsan.util.hadoop |
This package contains utility classes for hadoopS.
|
| fr.ens.biologie.genomique.eoulsan.util.locker |
This package contain an advanced multi JVM lock system.
|
| fr.ens.biologie.genomique.eoulsan.util.r |
This package contain utility classes for R usage.
|
| uk.ac.babraham.FastQC.Report |