Every time I restart the computer the link for Atom stops working
I tried it myself and it worked perfectly, even after a reboot. Do you have multiple disks/partitions in you set up?

Anyway, to settle things once and for all, I suggest you to follow the steps pointed out here. Below is a copy&amp;paste.

With the Atom editor open, in the menu bar:

Click Atom >> Install Shell Commands



You should expect to see:



You do not need to restart the terminal.

If this solution didn't work, my last suggestion is to create an alias in your ~/.bash_profile. To do this, simply open ~/.bash_profile with a text editor and add somewhere the line:

alias atom='open -a Atom'

This should do the trick.

EDIT

I noticed that after a reboot, you must start Atom at least once before the atom command works - otherwise it won't be recognized as a command. I didn't notice it before because, while testing if the ln -s ... solution worked, I already opened Atom once. I honestly don't have a clue why this happens, but the last suggestion about adding an alias definitely solves this issue.