====== Installation of BEAST 1.5 ======

===== Additional librairies ===== 

Java, already installed.

===== Procedure =====

Here is the procedure to install BEAST:

  * After downloading the archive from the web in ''/home/bioubuntu'', decompressed it and move the newly created folder in ''/opt/bio/sources'':

<code bash>
% sudo mv BEAST_v1.5.3 /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/BEASTv1.5.3
% sudo chmod 755 /opt/bio/sources/BEASTv1.5.3
</code>

  * Once you are in ''/opt/bio/sources/BEASTv1.5.3'', you will find the startup scripts in ''bin/''; no modification is necessary. To make them available to all, it is easier to edit the ''/etc/profile'' file by adding the following lines:

<code bash>
#
# BEAST specific environment variables
#
PATH=/opt/bio/sources/BEASTv1.5.3/bin:$PATH
</code>

  * To add the BEAST applications to the Impilo application menu, you will need to edit the Xfce4 configuration file:

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

  * The three items to add for ''beast'' are :
    * Item: Launcher
    * Name: BEAST - beast
    * Command: beast

  * The three items to add for ''beauti'' are :
    * Item: Launcher
    * Name: BEAST - beauti
    * Command: beauti

  * The three items to add for ''loganalyzer'' are :
    * Item: Launcher
    * Name: BEAST - loganalyzer
    * Command: loganalyzer

  * The three items to add for ''logcombiner'' are :
    * Item: Launcher
    * Name: BEAST - logcombiner
    * Command: logcombiner

  * The three items to add for ''treeannotator'' are :
    * Item: Launcher
    * Name: BEAST - treeannotator
    * Command: treeannotator