Proper way of automatically adding indexes docker service with Gitlab CI

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I'm having trouble with finding a proper way migrating a mongo service. I could either build a custom image with baked in indexes or install docker in main image and add those indexes during startup.

I think that both ways are kinda sketchy. The first is good because it will work, but i think that such things like adding necessary indexes should be in Makefile.

The second second one is sketchy because Docker image should be as light as possible.

Is there a way to call commands in service containers from Gitlab CI file?

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