How to build bcl2fastq2 on Ubuntu 16 LTS

bcl2fastq build ubuntu 16 LTS.md

1. Make sure configure can find sys/stat.h:

Modify bcl2fastq/src/cmake/macros.cmake

Find the last block:

#
# Macro to find libraries, with support for static-only search
#
macro(bcl2fastq_find_header_or_die variable file)
find_file(${variable} ${file} HINTS ENV C_INCLUDE_PATH ENV CPATH ENV CPLUS_INCLUDE_PATH)
if    (${variable})
    message(STATUS "${file} found as ${${variable}}")
else  (${variable})
    message(FATAL_ERROR "Required header ${file} not found.")
endif (${variable})
endmacro(bcl2fastq_find_header_or_die)

And change the find_file function to include /usr/include/x86_64-linux-gnu/ (the location of sys/ in Ubuntu on amd64) thusly:

find_file(${variable} ${file} HINTS ENV C_INCLUDE_PATH ENV CPATH ENV CPLUS_INCLUDE_PATH PATHS /usr/include/x86_64-linux-gnu/)

2. Fix the source code to work with newer Boost versions

bcl2fastq/src/cxx/lib/io/Xml.cpp modify lines 172 and 180 to include the correct template:

boost::property_tree::write_xml(os, treeWithIndexAttributes, boost::property_tree::xml_writer_make_settings(' ' , 2));

to

boost::property_tree::write_xml(os, treeWithIndexAttributes, boost::property_tree::xml_writer_make_settings<ptree::key_type>(' ' , 2));

and likewise again on line 180

Explanation: Boost versions >= 1.56 changed the definition of the xml_writer_make_settings function template: http://www.boost.org/doc/libs/1_44_0/boost/property_tree/detail/xml_parser_writer_settings.hpp http://www.boost.org/doc/libs/1_58_0/boost/property_tree/detail/xml_parser_writer_settings.hpp

Thanks so much for this. It's nuts to me that Illumina would push source code that explicitly fails on Ubuntu when one of the primary reasons for getting the source code at all is that they only have RPMs for CentOS/RedHat distros... This fix worked for me, so thanks again.

Thank you so much, really appreciate it.

Thanks! You probably just saved me several hours of work.

I was trying to install the bcl2fastq v2.20.0.422 and it seems that I don't need to fix the 2nd part about boost version.

could this be fixed in the new version of bcl2fastq?

@qingpeng This may have been fixed recently -- I haven't built it lately. I will give a try, and also in Ubuntu 18 LTS and report back.

@simon-anders Glad to be able to repay the favor -- HTseq likewise saved me an incalculable amount of time and was indispensable in the creation of Mucor

@jblachly Thanks for this, I still needed @najoshi's export on Ubuntu 18 LTS. The source fix wasn't needed, though I think this was because I let configure download its own boost distribution, as their source files don't seem to have been updated.

Thanks for this. I just went through it on Ubuntu 20.04 and I only had to apply the fix in bcl2fastq/src/cmake/macros.cmake.
There was also a problem with zlib, which was resolved by
sudo apt-get install zlib1g-dev.

Thanks for this. I only needed the first fix as well in Ubuntu 16 LTS!

Correction: the "make" command failed. So I had to apply the second fix as well.