In order for something to be included in the depreciation calculation, it will need to be allowed to be capitalized. If you can capitalize it, you will be able to depreciate it over the useful life of the asset too. Installation costs are usually capitalized as are all costs which were necessary to bring the asset into a operational condition.
The amount that is used to calculate the depreciation is the whole figure that has been capitalized. In other words, if installation costs have been capitalized (which they should have), then yes they need to depreciated too.
I don’t find it particularly applicable for installation costs but bear in mind that you might need to depreciate the actual cost of an asset over X years (for example) and an “expense” that was capitalized (something that it was necessary for the asset to operate) over Y years if they have different useful lives.