Compiling Illumina bcl2fastq 2.20 on ubuntu with newer versions of boost
compiling the latest Illumina bcl2fastq2 version 2.20 and 2.19 on ubuntu 16.04.3 seems to yield the following error:
https://gist.github.com/moonwatcher/5698a70fe4be81d1277ee0296c4c8b0c
The error seems to stem from src/cxx/lib/io/Xml.cpp assuming that all non win32 systems use an old version of boost that did not templatize the boost::property_tree::xml_writer_make_settings function.
https://gist.github.com/moonwatcher/ab22ba80f7583d28282ebd8f1d9f7d23
Why Illumina makes such a preposterous assumption is besides the point but if you want to get bcl2fastq2 2.20.0 to build you can just do away with said assumption by applying this patch
https://gist.github.com/moonwatcher/ac1176971d6032fc9e0d4402e5a81333
For extra credit here is a zsh script for downloading, patching and building bcl2fastq2 2.20.0
https://gist.github.com/moonwatcher/2a97f1e1c795f99c390e608028587cc3
You still need to make sure your system has all the dependencies installed as documented in the code but you will end up with functioning binary bcl2fastq executable.