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こんにちは! I have read a text about a guy whose wife has a housedust allergie, and there is this sentence: 私だってあんまりほこりがたまっていたら気になるから、仕方がないと思ってやっているんだ。 What does 思ってやって mean here?

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This やる is a simple verb meaning "to do". やっているんだ is "(It's that) I'm doing it", where this 'it' refers to the thing this guy is doing. (It's not mentioned in your question, so see the previous context by yourself.) And 仕方がないと思って is modifying やっている like an adverb.

「仕方がない」と思ってやっているんだ。
(literally) Thinking "it cannot be helped", I'm doing it.
I'm (reluctantly) doing this because I know it's unavoidable.

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