====== Installation of Jalview 2.4 ======

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

Java, which is already installed.

===== Procedure =====

Here is the procedure to install Jalview:

  * Jalview is distributed as a binary installer. Create a folder in ''/home/bioubuntu'' to put ut in and move it to ''/opt/bio/sources''.

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

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

  * Once you are in ''/opt/bio/sources/jalview'', you need to be able to launch the installer:
<code bash>
% sudo chmod u+x install.bin
% sudo ./install.bin
</code>

  * Let the installer do its stuff with default settings **except** that the install location is set from ''/root/Jalview'' to ''/opt/bio/sources/jalview''.

  * Let's make the application available to everyone:
<code bash>
% sudo ln -s /opt/bio/sources/jalview/Jalview /usr/local/bin/jalview
</code>

  * To add Jalview in the Impilo application menu, you need to modify the Xfce4 configuration file:
<code>
% sudo xfce4-menueditor /etc/xdg/xfce4/desktop/menu.xml
</code>
  * The three things to add are :
    * Item: Launcher
    * Name: Jalview
    * Command: jalview