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:
Then to compile bcl2fastq-1.8.4:
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.
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
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
Figured it might save a few others a few hours of tinkering.