Installation of Bcl2Fastq Fails
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 :)
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If your system accepts RPMs, then that'll be easier than getting this compiled.
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.
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:
I have no idea how to fix this :(
Which perl are you using? As I recollect, Bcl2fastq v.1.x requires perl v.5.12.
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
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
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.