This answer is late, but I was having the same issue. I found something that works.
In eclipse Project Explorer, right click the project name -> select "Run As" -> "Maven Build..."
In the goals, enter spring-boot:run
then click Run button.
I have the STS plug-in (i.e. SpringSource Tool Suite), so on some projects I will get a "Spring Boot App" option under Run As. But, it doesn't always show up for some reason. I use the above workaround for those.
Here is a reference that explains how to run Spring boot apps:
Spring boot tutorial
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