It ain't pretty but this should work

my $directory =
  "${\$machine->work_dir}/subdir/${\$machine->software_version}/";
[download]

But as it stands perl sees your string as

my $directory =
  $machine."->work_dir/subdir/".$machine."->software_version}/";
[download]

So you might need to either change the users' interface or force a style on them and definitely not use a source filter.
HTH

_________
broquaint