Mobyle Viewers

This project stores the Mobyle Viewer components, definitions distributed by the Institut Pasteur that can be plugged into the Mobyle system.

Warning: these Viewer components can only be used in the yet-unreleased version 1.0 of Mobyle, and are currently tested. The use of the unreleased versions of Mobyle and Programs/Viewers is strongly discouraged outside testing and experimentation purposes...

What viewers are available?

Jalview

Jalview is a multiple alignment editor written in Java. The Mobyle component displays multiple alignments in the applet version

Archaeopteryx

Archaeopteryx (the successor to ATV) is a Java application based on the forester libaries for the visualization of annotated phylogenetic trees. The Mobyle component enables the display of Phylogenetic trees in the applet version.

VARNA

VARNA is Java lightweight Applet dedicated to drawing the secondary structure of RNA. The Mobyle component displays these secondary structure in the applet version.

How to install these viewers?

Once a Mobyle server has been installed in a MOBYLEHOME directory on the system, the program definitions (i.e., the xml files that describe them to the Mobyle system) are stored in two directories:
  • the MOBYLEHOME/Services/ directory which contains program (Programs/) and viewer (Viewers/) definitions that the administrator has downloaded from distributions,
  • and the MOBYLEHOME/Local/Programs directory which contains custom program definitions that have either been created de novo by the server owner, or that he modified to fit his own needs.
To install the current viewers (archaeopteryx, jalview and varna), please proceed as follow:
  • check out the XML files from the subversion repository
    svn co https://projets.pasteur.fr/svn/pasteur-viewers
    
  • download the required dependencies (applets and configuration files). For your convenience, they can be downloaded from here.
  • install in MOBYLEHOME/Services the list of XML files and dependencies. Ultimately, the listing of this folder should look like this:
    $ ls
    archaeopteryx  archaeopteryx.xml  jalview  jalview.xml  varna  varna.xml
    
  • run mobdeploy with the v switch to deploy the viewers.
  • reload the portal in your web browser!