We developed Eoulsan, a versatile framework based on the Hadoop implementation of the MapReduce algorithm, dedicated to high throughput sequencing data analysis on distributed computers. With Eoulsan, users can easily set up a cloud computing cluster and automate the analysis of several samples at once using various software solutions available. Working either on standalone workstations or cloud computing clusters, Eoulsan provides an integrated and flexible solution for RNA-Seq data analysis of differential expression.
Eoulsan 2.0 is currently under development, however this version has successfully passed our integration tests and will generate the same outputs obtained with Eoulsan 1.2.2.
Warning: this documentation may not be up to date for the latest features of Eoulsan 2.0.
The main new features in this version of Eoulsan are:
You can now easily run Eoulsan using Docker with a dedicated eoulsan-docker.sh script that automatically configure your Docker environment like Eoulsan resources mounts. For more information about Docker and Eoulsan see the the related Eoulsan documentation. To install this script just copy and paste the following command line in your terminal:
$ curl http://outils.genomique.biologie.ens.fr/eoulsan2/eoulsan-docker-installer.sh | bash
Only few Eoulsan modes are currently working with the current version. The following table summarize the status of each mode:
|Eoulsan Mode||Action name||Status|
|Hadoop mode||hadoopexec||Working, Hadoop 2.x is required|
|Grid mode||gridexec||Planned, prototype works, waiting the Hadoop mode achievement|
|Amazon EMR mode||emrexec||Not working, dedicated code must be rewritten for the new workflow engine|
|Other cloud mode||not defined||Planned, implementation not started|
Note: Eoulsan 2.x is not binary compatible with Eoulsan 1.2.x, so step plug-ins written for previous versions will not work this release. The Eoulsan 2.x API is not currently stable and breaking compatibility may occurs until final Eoulsan 2.0 version.
The following screencast show how to install Eoulsan, create a design file and launch an analysis in local mode. For more information see the quickstart guide.
Eoulsan contains out the box a fully customizable RNA-Seq pipeline that generate many reports about the performed analysis. The following images are samples of the graphics generated by the normalization and differential analysis steps:
This version currently use DESeq 1 for normalization and differential analysis but support of DESeq 2 is planned latter in the Eoulsan 2.0 release cycle.
The final Eoulsan 2.0 version will support Chip-Seq analysis, however this feature is currently not implemented.
Eoulsan contains also a java object model that can be used outside the Eoulsan workflow engine to handle and manipulate NGS data. See the Eoulsan developer wiki for more informations about this part of the project.
This work was supported by the Infrastructures en Biologie Santé et Agronomie (IBiSA), France Genomique and Amazon Web Services research grant.