When setting up Ubuntu/Debian machines for biology, I sometimes need to have HTSlib installed separately from SAMtools. I also need this done automatically, without my intervention (E.G.: for the creation of Amazon Machine Images). To do this, I do the following as Root.

  1. Make sure that HTSlib’s prerequisites are installed. 
     apt-get install autoconf automake make gcc perl zlib1g-dev libbz2-dev liblzma-dev libcurl4-gnutls-dev libssl-dev
  2. Make a new directory where you want to install HTSlib and navigate to it.
  3. Run the following commands to grab the .tar.bz2 file from Github, untar it and install it. 
     curl -s https://api.github.com/repos/samtools/htslib/releases/latest \
     | grep '"browser_download_url":.*bz2"$' \
     | awk '{print $2}' \
     | xargs wget
 tar -xvf *.bz2
 cd $(ls -d */)
 autoreconf -i
 ./configure
 make
 make install

This can optionally be tested with pkg-config --exists htslib && echo OK