How to make Latexmk use makeglossaries?

At Hans-Peter E. Kristiansen’s request, I provide another answer, extending the one given by kay102.

Add the following lines to some latexmk initialization file (e.g., on Linux systems, ~/.latexmkrc):

add_cus_dep('glo', 'gls', 0, 'run_makeglossaries');
add_cus_dep('acn', 'acr', 0, 'run_makeglossaries');

sub run_makeglossaries {
  if ( $silent ) {
    system "makeglossaries -q '$_[0]'";
  }
  else {
    system "makeglossaries '$_[0]'";
  };
}

As a consequence, if latexmk is invoked with the -silent option makeglossaries will be silent, too.

Moreover, add

push @generated_exts, 'glo', 'gls', 'glg';
push @generated_exts, 'acn', 'acr', 'alg';
$clean_ext .= ' %R.ist %R.xdy';

to update the cleanup functionality of latexmk appropriately.

You need to write a configuration file that tells latexmk which files are interesting for the glossary and how to handle them. Fortunately, the author provides some sample rc files.

Putting

add_cus_dep('glo', 'gls', 0, 'makeglo2gls');
sub makeglo2gls {
    system("makeindex -s '$_[0]'.ist -t '$_[0]'.glg -o '$_[0]'.gls '$_[0]'.glo");
}

in ~/.latexmkrc (globally in your home directory) or ./latexmkrc (locally in your document directory) should do the trick.

You can also let latexmk call makeglossaries directly by adding the following to your latexmkrc file (in my case I had to add it to $HOME/.latexmkrc):

add_cus_dep('glo', 'gls', 0, 'makeglossaries');
add_cus_dep('acn', 'acr', 0, 'makeglossaries');

sub makeglossaries {
    system "makeglossaries $_[0]";
    if ( -z "$_[0].glo" ) {
        open GLS, ">$_[0].gls";
        close GLS;
    }
    return 0;
}