This NOT a copy of Can't use Segger J-link in Eclipse
He was able to solve his issue, and the solution does not work for me. I have installed Segger J-Link version 6.14, but the IDE is not displaying it under Windows->Preferences->Run/Debug as it supposedly should. PLEASE help.
Since no one has bothered answering and this MAY be useful to some other poor soul:
Try updating Eclipse GNU ARM tool chain from source forge.
In my case Source forge was acting up and I couldn't download the the utility properly. Hence the whole issue; if you do face this issue such as "unable to read from repository" or "handshake failed" it could be an issue with the JDK in your system: http://gnuarmeclipse.github.io/blog/2017/01/29/plugins-install-issue/
The above link solved my issue with the Java environment and I was able to properly update Eclipse.
Once the tool chain was updated the Segger J-Link option appeared in the Run/Debug section and everything was right as rain.
Hope this helps.