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! 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.