Dear Alex, As the Perl transition is over, I have updated libbam to serve its headers in /usr/include/samtools, and libbio-samtools-perl to search for them there. You can go ahead with a similar change in cufflinks any time you like. Have a nice day, -- Charles Plessy Debian Med packaging team, http://www.debian.org/devel/debian-med Tsurumi, Kanagawa, Japan