Java, already installed.

Here is the procedure to install ReadSeq:

• ReadSeq is distributed as a JAR archive, ready for execution. Create a folder in /home/bioubuntu to put the archive in and move this folder to /opt/bio/sources.

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

% sudo chown -R root:root /opt/bio/sources/readseq-2.1.19-src
% sudo chmod 755 /opt/bio/sources/readseq-2.1.19-src

• Once you are in /opt/bio/sources/readseq-2.1.19-src, create two small scripts to make your life easier:

% sudo touch readseq
% sudo touch readseq_gui

• For readseq, put the following code:

#!/bin/sh
java -cp /opt/bio/sources/readseq-2.1.19-src/readseq.jar run

• For readseq_gui, put the following code:

#!/bin/sh
java -cp /opt/bio/sources/readseq-2.1.19-src/readseq.jar app

• You need to make them executable and available to all:

% sudo chmod ugo+x readseq
% sudo ln -s /opt/bio/sources/readseq-2.1.19-src/readseq /usr/local/bin/readseq
% sudo chmod ugo+x readseq_gui
% sudo ln -s /opt/bio/sources/readseq-2.1.19-src/readseq_gui /usr/local/bin/readseq_gui

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

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

• The three things to add are:
  • Item: Launcher
  • Name: Readseq
  • Command: readseq_gui