====== Installation of FigTree 1.3.1 ======

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

Java, already installed.

===== Procedure =====

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'':

<code bash>
% sudo mv FigTree_v1.3.1 /opt/bio/sources
</code>

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

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

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

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

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

<code bash>
% 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
</code>


  * To add FigTree in the Impilo application menu, you need to edit the Xfce4 configuration file:

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

  * The three items to add are :
    * Item: Launcher
    * Name: FigTree
    * Command: figtree