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====== Installation of Cytoscape 2.6.3 ======

===== Additional libraries =====

Java, already installed.

===== Procedure =====

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''.

<code bash>
% sudo mv /home/bioubuntu/cytoscape-v2.6.3 /opt/bio/sources
</code>

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

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

  * 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:

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

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

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

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

<code bash>
% sudo xfce4-menueditor /etc/xdg/xfce4/desktop/menu.xml
</code>

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