Java, already installed.

Here is the procedure to install Mesquite:

• After downloading the Mesquite archive from the web, it is decompressed in /home/bioubuntu and moved in /opt/bio/sources:

% sudo mv Mesquite_Folder /opt/bio/sources

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

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

• The startup script run_mesquite.sh needs to be edited for the script to work in Impilo. To be on the safe side:

% sudo cp /opt/bio/sources/Mesquite_Folder/run_mesquite.sh /opt/bio/sources/Mesquite_Folder/run_mesquite.sh.bck

• Use a text editor to open run_mesquite.sh and remove all of its content to put the following lines instead:

#!/bin/bash
MESQUITE_HOME=/opt/bio/sources/Mesquite_Folder
java -Djava.libray.path=lib -Djri.ignore.ule="yes" -Xmx256M -Xss4m -cp $MESQUITE_HOME mesquite.Mesquite $*

• To make the application available to all:

% sudo ln -s /opt/bio/sources/Mesquite_Folder/run_mesquite.sh /usr/local/bin/mesquite

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

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

• The items to add are :
  • Item: Launcher
  • Name: Mesquite
  • Command: mesquite