Create a new file named ${app-name}.desktop inside /home/$USER/.local/share/applications.
Modify the Desktop Entry according to your application and copy it inside ${app-name}.desktop.
[Desktop Entry]
Version=version-number
Name=program-name
Comment=what the application is
Exec=/home/username/path/to/application-launcher
Path=/home/username/path/to/application-folder/
Icon=/home/username/path/to/application-folder/icon.xpm
Terminal=false
Type=Application
Categories=Utility;Application;Development;
Then add execution permissions to it with chmod u+x ${app-name}.desktop.
Example of Eclipse Desktop Entry
[Desktop Entry]
Version=Oxygen
Name=Eclipse
Comment=Eclipse is an IDE
Exec=/home/turi/Applications/eclipse-version/eclipse
Icon=/home/turi/Applications/eclipse-version/icon.xpm
Terminal=false
Type=Application
Categories=Utility;Application;Development;