Java, already installed.

Here is the procedure to install FigTree:

• After downloading the archive the FigTree files, yo uhave to decompressed it in /home/bioubuntu and move the newly created folder in /opt/bio/sources:

% sudo mv FigTree_v1.3.1 /opt/bio/sources

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

% sudo chown -R root:root /opt/bio/sources/FigTree_v1.3.1
% sudo chmod 755 /opt/bio/sources/FigTree_v1.3.1

• The figtree script found in /opt/bio/sources/FigTree_v1.3.1/bin needs to be edited to make it work in Impilo:

#!/bin/sh
FIGTREE_HOME=/opt/bio/sources/FigTree_v1.3.1
java -Xms64m -Xmx512m -jar $FIGTREE_HOME/lib/figtree.jar $*

• To make it available to all, do the following steps:

% sudo chmod 755 /opt/bio/sources/FigTree_v1.3.1/bin/figtree
% sudo ln -s /opt/bio/sources/FigTree_v1.3.1/bin/figtree /usr/local/bin/figtree

• To add FigTree in 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: FigTree
  • Command: figtree