Setup

Add this to ~/.latexmkrc:

add_cus_dep('acn', 'acr', 0, 'makeacn2acr');
sub makeacn2acr {
    system("makeindex -s \"$_[0].ist\" -t \"$_[0].alg\" -o \"$_[0].acr\" \"$_[0].acn\"");
}