Creating a .desktop file for a new application

For reference see the Freedesktop Desktop Entry Specification, but this should work:

[Desktop Entry]
Version=1.0
Name=Unipro UGENE
Comment=Unipro UGENE is a cross-platform visual environment for DNA and protein sequence analysis.
Exec=/home/samuel/ugene-1.11.5/ugene -ui
Path=/home/samuel/ugene-1.11.5/
Icon=/usr/share/icons/Humanity/apps/32/access.svg
Terminal=false
Type=Application
Categories=Utility;Development;

Some notes:

Version

• Should be 1.0, it refers to the .desktop file version, not to the program version.

Name

• The name that should be displayed on the menu.

Exec

• The full path to the executable. No need to use '.', it just means the current dir

Path

• The dir that will be set as current when the entry is run. You usually don't need to set it, but I have added it just in case. It is the same as using 'cd' in your command line

Icon

• The path to the icon file that will be used for the file, it's likely that the one that you put doesn't exists, I have changed it for a generic one. You should change this to the file that you want the icon to use

Mimetype

• Specifies the kind of files that this program is able to open. I've left it empty.

StartupWMClass

• Only needed for some programs, It is usually needed by java programs but only set it if you notice some problems.

To use the desktop file from the Dash you will need to copy it to /usr/share/applications for any user to be able to use it (you will need administrator permissions) or to ~/.local/share/applications (where ~ means your user directory) if you just want it to be available for one user.

Instead of manually adding .desktop files, you can use the little GUI tool alacarte (Main Menu) to do this for you.

Installation:

sudo apt install alacarte