Add via command line application in "Applications Log In"

Hello, one way to do this without using the UI is to put the shortcut (with .desktop extension) of your software in the ~/.config/autostart/ folder, everything inside this folder will run in initialization of the UI. You can create a .desktop file like this:

[Desktop Entry]
Version=1.0
Name=my Unipro UGENE
GenericName=Integrated Bioinformatics Suite
Comment=Unipro UGENE is a cross-platform visual environment for DNA and protein sequence analysis.
MimeType=text/english;text/plain;text/x-makefile;text/x-c++hdr;text/x-c++src;text/x-chdr;text/x-csrc;text/x-java;text/x-moc;text/x-pascal;text/x-tcl;text/x-tex;application/x-shellscript;text/x-c;text/x-c++;
Exec=/home/samuel/ugene-1.11.5 ./ugene -ui -c %F
Icon=/usr/share/icons/hicolor/scalable/apps/ugene.svg
Type=Application
Terminal=true
Categories=Utility;Development;
StartupWMClass=UGENE

See more about .desktop files at: link

This is the only way to do this without using the UI that I know, I hope I have helped.

PS: If you want to initialize a service at system startup (not necessarily UI), take a look at the Daemons and Init Scripts .