Compiling bcl2fastq v2.15 on Ubuntu 12.04 and 14.04

I thought I'd start here since the packages are more up to date (turns out it's a good thing I did, see the morass below). There's some documentation from Illumina for compiling from source here. There's not a lot to go on, other than a list of dependencies, which boils down to:

• zlib
• librt
• libpthread
• gcc 4.1.2 (with c++)
• boost 1.54 (with its dependencies)
• cmake 2.8.9

Really the only tricky part was figuring out the required packages, which didn't correspond particularly well to the list of dependencies above. I didn't bother trying to install specific version of any of the dependencies other than boost 1.54.

On an Amazon AWS EC2 instance (m3.medium, ubuntu-trusty-14.04-amd64-server-20140607.1 ami-e7b8c0d7):

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install zlibc
sudo apt-get install libc6 # provides librt and libpthread
sudo apt-get install gcc
sudo apt-get install g++
sudo apt-get install libboost1.54-all-dev
sudo apt-get install cmake

From there, compilation more or less works as advertised:

wget ftp://webdata2:webdata2@ussd-ftp.illumina.com/downloads/Software/bcl2fastq/bcl2fastq2-v2.15.0.4.tar.gz
tar -xf bcl2fastq2-v2.15.0.4.tar.gz
cd bcl2fastq
mkdir build
cd build
PREFIX=/usr/local
sudo mkdir -p ${PREFIX:?}
../src/configure --prefix=${PREFIX:?}
make
sudo make install

We wanted this version to coexist with an older one, so I renamed the executable:

sudo mv $PREFIX/bin/bcl2fastq $PREFIX/bin/bcl2fastq2

Emboldened, I went on to 12.04. This was a lot more painful. Lots of trail and error. Here's what I came up with. More or less the same as above at first (m3.medium, ubuntu-precise-12.04-amd64-server-20140717 ami-23f78e13):

sudo apt-get update
sudo apt-get upgrade
sudo apt-get install zlibc
sudo apt-get install libc6 # provides librt and libpthread
sudo apt-get install gcc
sudo apt-get install g++

We'll also need libboost version 1.54; to do this, we need to add a third-party ppa (https://launchpad.net/~boost-latest/+archive/ubuntu/ppa).

sudo apt-get install python-software-properties
sudo add-apt-repository ppa:boost-latest/ppa
sudo apt-get update
sudo apt-get install libboost1.54-all-dev

I tried to install cmake 2.8.9 from various ppa's but kept getting errors when I compiled bcl2fastq. So, source it is.

sudo apt-get build-dep cmake
wget http://www.cmake.org/files/v2.8/cmake-2.8.9.tar.gz
tar -xf cmake-2.8.9.tar.gz
cd cmake-2.8.9
./configure && make && sudo make install

Finally, an error complaining about the absence of sys/stat.h. I found good advice here:

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

After all of that, compiling bcl2fasta worked as described for 14.04.