To use the Illumina support in Run Scanner, the additional package runscanner-illumina must be built.

You will need a copy of jsoncpp and an AutoTools-capable build environment with libstdc++ 5 or later. On Debian/Ubuntu:

sudo apt-get install pkg-config cmake libjsoncpp-dev autoconf libtool build-essential clang-12

On Fedora/Red Hat:

sudo yum groupinstall "Development Tools"
sudo yum install pkgconfig cmake jsoncpp-devel libtool autoconf clang

Note: Some metrics will be formatted based on the machine's locale preferences, so you may want to check those via the locale command (on most systems).

Pull the Illumina Interop code via:

git submodule init && git submodule update

Then:

cd runscanner-illumina && ./build-illumina-interop && autoreconf -i && ./configure && make && make install

After which, deploy Run Scanner as directed in Installation & Setup.

Note that Run Scanner expects to be able to find the runscanner-illumina program on the path. For Debian and Ubuntu systems, in /etc/init.d/tomcat8, adjust the PATH to include /usr/local/bin.