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This is actually quite easy. SA is auto-detected when you install qmail-scanner, and uses the spamd/spamc combo if available. Here is my configure line (sans private data):
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#$ ./configure --spooldir /var/lib/qmailscan --qmaildir /var/qmail --bindir /var/qmail/bin \ --qmail-queue-binary /var/qmail/bin/qmail-queue --admin postmaster@example.com --domain example.com \ --notify none --local-domains example1.com,example3.com,some.other.domain.net --silent-viruses auto \ --lang de_DE --debug 1 --unzip 0 --add-dscr-hdrs 0 --archive 1 --redundant no --log-details \ --fix-mime 1 --scanners "verbose_spamassassin" --install 1 |