Java, already installed.

Here is the procedure for installing PathVisio:

• PathVisio is distributed as a Java Web Start file. Create a folder under /home/bioubuntu and move the pathvisio.jnlp file in it; after, move this folder to /opt/bio/sources.

% mkdir /home/bioubuntu/pathvisio
% mv pathvisio.jnlp /home/bioubuntu/pathvisio
% sudo mv /home/bioubuntu/pathvisio /opt/bio/sources

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

% sudo chown -R root:root /opt/bio/sources/pathvisio
% sudo chmod 755 /opt/bio/sources/pathvisio

• Once you are in /opt/bio/sources/pathvisio, simply create a script named pathvisio which will contain the following lines:

#!/bin/sh
javaws /opt/bio/source/pathvisio/pathvisio.jnlp

• This script needs to be available to all:

% sudo chmod ugo+x pathvisio
% sudo ln -s /opt/bio/sources/pathvisio/pathvisio /usr/local/bin/pathvisio

• To add Pathvisio to the Impilo application menu, you need to edit the Xfce4 configuration file:

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

• The three items to add are:
  • Item: Launcher
  • Name: PathVisio
  • Command: pathvisio

• At first launch, Java Web Start wil ask you if you trust the Pathvisio site. Yes is the correct answer