Java, already installed.

Here is the procedure to install Cytoscape:

• Cytoscape is distributed as a JAR archive ready to use. Download the archive version (not the one with a JRE with it: we already have a functioning Java installation), decompressed under /home/bioubuntu and move this folder into /opt/bio/sources.

% sudo mv /home/bioubuntu/cytoscape-v2.6.3 /opt/bio/sources

• This folder should belong to root and its permissions set to 755.

% sudo chown -R root:root /opt/bio/sources/cytoscape-v2.6.3
% sudo chmod 755 /opt/bio/sources/cytoscape-v2.6.3

• Once you are in /opt/bio/sources/cytoscape-v2.6.3, you have to modify a script called cytoscape.sh to put the following content:

#!/bin/sh
CYTOSCAPE_HOME=/opt/bio/sources/cytoscape-v2.6.3
java -Dswing.aatext=true -Xss5M -Xmx512M -jar $CYTOSCAPE_HOME/cytoscape.jar cytoscape.CyMain -p plugins "$@"

• Since the script is already executable, you only need to make it available to all:

% sudo ln -s /opt/bio/sources/cytoscape-v2.6.3/cytoscape.sh /usr/local/bin/cytoscape

• To add Cytoscape in the Impilo application menu, edit the Xfce4 configuration file:

% sudo xfce4-menueditor /etc/xdg/xfce4/desktop/menu.xml

• The three things to add are :
  • Item: Launcher
  • Name: Cytoscape
  • Command: cytoscape