Installation of BEAST 1.5

Java, already installed.

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:

% sudo mv BEAST_v1.5.3 /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/BEASTv1.5.3
% sudo chmod 755 /opt/bio/sources/BEASTv1.5.3

• 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:

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

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

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

• 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