Installing demultiplexing such as bcl2fastq, CellRanger, LongRanger, demuxlet, and whatever else pops up, holds a special place in those that do Bioinformatics and Genomics hearts and potentially therapy sessions. It has been enough of an issue in my professional life that I thought I would dedicate a series to setting up servers for different analysis types.
This is my big chance to go on a total rant about bioinformatics servers!
Don't install all kinds of software as system packages. Ok? Just don't do it. It may not backfire on you today, or tomorrow, but someday it will!
I'm going to make a few caveats to that. Things like zlib, openssl, and ssh are fine. I'll even cheat sometimes and yum install some development tools. Mostly, what I am talking about here is bioinformatics software. Don't bother installing bcl2fastq, blast, augustus, R, python, dask, or pretty much anything else as system dependencies.