Dimont

by Jan Grau, Stefan Posch, Ivo Grosse, and Jens Keilwagen

ChIPper is a universal tool for de-novo motif discovery. ChIPper has successfully been applied to ChIP-seq, ChIP-exo and protein-binding microarray (PBM) data.

We provide ChIPper as a public web-server, a web-application that can be installed in a local Galaxy server, and as a command line program.

ChIPper web-server

ChIPper is available as a public web-server at galaxy.informatik.uni-halle.de.

Download

ChIPper is implemented in Java using Jstacs. You can download the command line application as a Jar. In addition, we provide the Jar of the Galaxy web-application for installing it in your local Galaxy server.

ChIPper will be part of the next public release of the Jstacs library.

Running the command line application

For running the command line application, Java v1.6 or later is required.

The arguments of the command line application have the following meaning:

Installing the web-application

The command-line program behind the web-application is a Jar as well, so Java is required on the server running Galaxy. To install this command line program in Galaxy, copy it to the desired destination in the Galaxy tools directory.

The command line application writes its Galaxy tool definition file itself. If you are in the directory containing the command-line program for Galaxy, you can create the tool definition file by calling

java -jar ChIPperWeb.jar --create ChIPperWeb.xml

Afterwards, this directory contains the tool definition file ChIPperWeb.xml. Now you can register ChIPper in the Galaxy tool_conf.xml file. For details, see the Galaxy tutorial for adding new tools.