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Old 04-23-2014, 12:49 AM   #1
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Location: California

Join Date: Apr 2014
Posts: 1
Default 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:
$ 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:
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.
BBroadley is offline   Reply With Quote

bcl2fastq, boost, debian, ubuntu

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