(2) and (4) are certainly wrong.
I felt uncomfortable with the use of 'such that ...' (which is normally adjectival) to stand in for the standard adverbial 'in such a way that ...' in the other sentences. I was not surprised by this comment from the AHD:
Usage Note: The adjective such is often followed by that when such is
used to mean "of a degree or quality indicated," as in the sentence
The demand of Feinberg's specialized services is such that he commands
around $200,000 a month when he gets involved in a case. This example
is acceptable to 87 percent of the Usage Panel. · The Panel does not,
however, find the phrase such that to be an acceptable replacement for
so that or in such a way that. A mere 12 percent approve of this usage
in the sentence The products are packaged [/ We package the products] such that users can pick the
components they need and add capabilities over time.
so I'd opt for:
We have set up the tool in such a way that a raised alarm will stop
the whole analysis.