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.