====== Installation of NJPlot 2.3 ======

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

   * ''lesstif2'' 
   * ''ncbi-data'' 
   * ''libncbi6-dev'' 
   * ''libvibrant6-dev''

<code bash>
% sudo apt-get -y install lesstif2 ncbi-data libncbi6-dev libvibrant6-dev
</code>

===== Procedure =====

Here is the procedure to install NJPlot from source code:

  * The archive with the source code is downloaded from the web in ''/home/bioubuntu'', decompressed and the newly created folder is moved in ''/opt/bio/sources''.

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

<code bash>
% sudo mv njplot-2.3 /opt/bio/sources
% sudo chown -R root:root /opt/bio/sources/njplot-2.3
</code>

  * Once you are in ''/opt/bio/sources/njplot-2.3'', you need to edit the ''makefile'' file by changing the following lines with new values:

<code bash>
#uncomment and locally adapt next line to fix the full helpfile path name
HELPFILENAME = -DHELPFILENAME=\"/opt/bio/sources/njplot-2.3/njplot.help\"

# Vibrant top directory
VIBRANT = /usr/include/ncbi

# motif library directory
MOTIFLIB = /usr/lib
MOTIFINCL = /usr/include
</code>

  * NJPlot is easily compiled:

<code bash>
% sudo make
</code>

  * To make these applications available to all:
<code bash>
% sudo ln -s /opt/bio/sources/njplot-2.3/njplot /usr/local/bin/njplot
% sudo ln -s /opt/bio/sources/njplot-2.3/newicktops /usr/local/bin/newicktops
% sudo ln -s /opt/bio/sources/njplot-2.3/newicktotxt /usr/local/bin/newicktotxt
% sudo ln -s /opt/bio/sources/njplot-2.3/unrooted /usr/local/bin/unrooted
</code>

  * Il faut maintenant ajouter NJPlot dans le menu Impilo:
<code>
% sudo xfce4-menueditor /etc/xdg/xfce4/desktop/menu.xml
</code>

  * Les trois chose à inscrire sont :
    * Item: Launcher
    * Name: NJPlot
    * Commande: njplot