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  • bcl2fastq-1.8.4 on debian/ubuntu solution

    I was frustrated to find very little useful documentation on getting bcl2fastq (released in 2013) working boost newer than August 2010.

    Seems kinda odd for a program so heavily dependent on boost to ignore all the boost releases since Nov 2010.

    I tried to get it to work with various newer boost's without luck. The included boost-1.44.0 has numerous issues with more recent compilers and libraries.

    So my solution (gross as it is) for boost is:
    Code:
    $ sudo apt-get install build-essential g++ g++-4.6
    $ cd /opt/src
    $ tar xvjf bcl2fastq-1.8.4.tar.bz2
    $ mv bcl2fastq bcl2fastq-1.8.4
    $ tar xvzf bcl2fastq/redist/boost_1_44_0.tar.gz
    $ cd boost_1_44_0
    $ find . -type f -exec perl -pi -e 's/TIME_UTC/TIME_UTC_/g' {} \;
    $ echo "using gcc : 4.6 : /usr/bin/g++-4.6 ; " >> tools/build/v2/user-config.jam
    vi ./boost/config/stdlib/libstdcpp3.hpp
    line 36:
    c   || defined(_GLIBCXX__PTHREADS) \
    +   || defined(_GLIBCXX_HAS_GTHREADS)
    bjam --toolset=gcc-4.6 --prefix=/share/apps/boost-1.44.0 -j 6 install
    Then to compile bcl2fastq-1.8.4:
    Code:
    mkdir bcl2fastq-build
    cd  bcl2fastq-build
    export BOOST_ROOT=/share/apps/boost-1.44.0
    ../bcl2fastq-1.8.4/src/configure --prefix=/share/apps/bcl2fastq-1.8.4 --verbose
    make -j 6
    make -j 6 install
    I'm not done testing, but at least it seems to build, and the default testing of the binaries seems to be working without problem.

    Figured it might save a few others a few hours of tinkering.

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