Guix provides build system abstractions like `gnu-build-system` for traditional build systems, but you can easily override or extend the build phases. You can

Guix provides build system abstractions like `gnu-build-system` for traditional build systems, but you can easily override or extend the build phases. You can run scripts with `(invoke "my-script.sh")`. The bigger problem, in my opinion, is that packages that use custom build systems often have strange ideas about what is desirable in a build system. Sometimes they prefer to download things during the build (that's not permitted in Guix) or they will make assumptions about the layout of directories or the discovery of dependencies. Patching away all of these invalid assumptions can be annoying, but it is possible as is demonstrated in many package definitions in the `(gnu packages bioinformatics)` module.