Installation of Bcl2Fastq Fails

Question

[dec986]

I am trying to install Illumina's bcl2fastq but I am getting errors I can't find solutions to:

-- Found Doxygen: /usr/bin/doxygen 
-- Doxygen: /usr/bin/doxygen. Dot: DOXYGEN_DOT_EXECUTABLE-NOTFOUND.
-- Creating Doxygen config file: /home/con/Downloads/bcl2fastq_v1.8.4/src/c++/Doxyfile
-- Configuring incomplete, errors occurred! Couldn't configure the project

Google doesn't have anything on this... and Illumina technical support is very very slow... does anyone know how to solve this?

thanks :)

[Devon Ryan]

If your system accepts RPMs, then that'll be easier than getting this compiled.

[GenoMax]

What sequencer are you hoping to process the data from? If that is NextSeq 500 or HiSeq 3K/4K then you should get the new version of bcl2fastq (v. 2.17.x). As @Devon said use the RPM if you can.

[dec986]

As Devon suggested, I downloaded the RPM, and am trying to convert to deb but this fails:

con@e:~/Downloads/bcl2fastq_v1.8.4$ fakeroot alien bcl2fastq-1.8.4-Linux-x86_64.rpm Unpacking of 'bcl2fastq-1.8.4-Linux-x86_64.rpm' failed at /usr/share/perl5/Alien/Package/Rpm.pm line 168.

I looked at the line 168:

$this->do("rpm2cpio '".$this->filename."' | (cd $workdir; $decomp cpio --extract --make-directories --no-absolute-filenames --preserve-modification-time) 2>&1")
    or die "Unpacking of '".$this->filename."' failed";

I have no idea how to fix this :(

[GenoMax]

Which perl are you using? As I recollect, Bcl2fastq v.1.x requires perl v.5.12.

[dec986]

hi genomax2,

I'm using 5.22.1, I tried this, as you said,

use 5.12.0;

but it outputs Name "Alien::Version" used only once: possible typo at alien.pl line 375.

and no output file. I comment this line out, and nothing happens.

-still stuck

[GenoMax]

I suggest that you get bcl2fastq v.2.17.x. It is backwards compatible with all sequencer types and should install easier than v.1.x.

That said see if these two threads help: http://seqanswers.com/forums/showthread.php?t=45649
http://seqanswers.com/forums/showthread.php?t=45649

[Devon Ryan]

Do you just have to demultiplex stuff this one time or is this going to be a regular thing? If this is just a one-off instance, then it might be simplest to setup a Centos-based docker container and directly install bcl2fastq in it. You could then demultiplex stuff inside the container. Yes, this seems convoluted, but it might prove quicker.