Teresita M. Porter - Install bcl2fastq on Ubuntu

10 - Installing bcl2fastq 1.8.4 on Ubuntu 12.04.5

When .bcl files were generated with Illumina RTA < 1.18.54, the older bcl2fastq v1.8.4 needs to be used to convert base calls to fastq files. Since Illumina does not provide a package that can be installed by apt-get on Ubuntu, I've compiled the steps I had to take to get this older software up and running.

To start with, I mostly followed the instructions available here and I outline the steps that I took below to make the process easy to follow from the very start.

sudo apt-get update

sudo apt-get upgrade

sudo apt-get install zlibc

sudo apt-get install libc6

sudo apt-get install gcc

sudo apt-get install g++

sudo apt-get install python-software-properties

sudo apt-get build-dep cmake

cmake was installed from source as follows:

wget http://www.cmake.org/files/v2.8/cmake-2.8.9.tar.gz

tar -xvf cmake-2.8.9.tar.gz

cd cmake-2.8.9

./configure && make && sudo make install

Then I added a bunch of symbolic links to library files:

sudo mkdir -p /usr/include/sys

sudo ln -s /usr/include/x86_64-linux-gnu/sys/stat.h /usr/include/sys/stat.h

sudo ln -s /usr/include/x86_64-linux-gnu/libz.so /usr/lib/libz.so

sudo ln -s /usr/include/x86_64-linux-gnu/libbz2.so /usr/lib/libbz2.so

sudo ln -s /usr/lib/x86_64-linux-gnu/libpthread* /usr/lib

I also needed to install libxml2:

sudo apt-get install libxml2 libxml2-dev

Because the Illumina software is sensitive to the version of boost installed, I had to retrieve the older boost 1.44, install it manually, and add symbolic links.

wget boost_1_44_0.tar.gz "https://sourceforge.net/projects/boost/files/boost/1.44.0/boost_1_44_0.tar.gz"

tar -xvf boost_1_44_0.tar.gz

cd boost_1_44_0

sh bootstrap.sh

./bjam

sudo ln -s /path/to/boost_1_44_0/stage/lib /usr/lib

sudo ln -s /path/to/boost_1_44_0 /usr/include

Now to actually install bcl2fastq 1.8.4, the linux tarball can be downloaded from the Illumina site here. Manually install as follows:

tar -xvjf bcl2fast1-1.8.4.tar.bz2

cd bcl2fastq

mkdir build

cd build