@magnetophon, I'm not sure how exactly I can be of further help here.

>From what I understand, NixOS requires a lot of file path patching, from the 
>output of configure, to paths hardcoded in Makefiles, and paths in scripts.

At the very least, you'll need /usr/bin/env.
I'll happily take patches like this:

    -#!/usr/bin/python2.7
    +#!/usr/bin/env python2.7

And similar things could be applied to configure.ac, but paths hardcoded in the 
generated configure due to macros from /usr/share/autoconf/... are not under 
Beast's control. That simply requires significant porting effort on NixOS and 
should arguably be fixed/adapted by the NixOS autoconf + automake packages. If 
that was fixed on NixOS, it'd be much easier to simply build Beast via 
autogen.sh from git release tags, using autoconf and automake from NixOS 
instead of paths hardcoded in tarbals for regular unix systems.
Our git tags are guaranteed to match the released tarballs, so you'd get the 
same release code base there, but with fewer hard coded paths. Of course that 
requires a *working* git setup, including git log and git describe, and 
unfortunately NixOS intentionally doesn't even provide that for package builds. 
At least not easily... ;-(
 
With every package in NixOS having their own bin/ directory, I also wonder how 
NixOS wants to scale up to supporting hundreds or thausands of package 
installations...

In any case, the paths have to be adjusted first (though I suspect that to be a 
pretty fragile undertaking that could break packages fairly often). If that's 
done the Makefile rules should also properly work so file generation rules will 
be properly carried out.

I'm always on IRC of course, but is there a point in keeping this bug report 
open?

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