[GenoMax]

Yes, I'm reading the documentation from here:

http://supportres.illumina.com/documents/documentation/software_documentation/bcl2fastq/bcl2fastq_letterbooklet_15038058brpmi.pdf

It actually complains that the SampleSheet does not have the correct format:

configureBclToFastq.pl --input-dir Data/Intensities/BaseCalls --output-dir Unaligned --positions-format .locs --no-eamss
"ERROR: Wrong number of fields in sample sheet (expected: 10, got 2: IEMFileVersion,4)"

Good to know someone is using the software for MiSeq... there's still hope then.

Thanks,
Daniel

I am going to let you go through what I posted in the new thread you started. Let us work through that thread since your problem is no longer about installation. We can fix the samplesheet easily.

Once you respond to the questions in the other thread we can continue.

[dsobral]

Thanks. I'm continuing this in the other thread:

http://seqanswers.com/forums/showthread.php?t=39153

Daniel

[roko-t]

I　had the confusing trouble at the installing for Hiseq v4 but I solved it. (^^)
In my case it was because of the Boost library version and the incompatibility with gcc in my default environment on Linux.

The following version set is NG.
Boost C++ library v 1.55.0 or v 1.44.0
gcc 4.8.1, with c++

The following version set is OK !!
Boost C++ library v 1.44.0
gcc 4.6.2, with c++

We need to set the following environment variables to use specified　Boost and gcc for configuring the build.
CC
CXX

BOOST_ROOT #location of the boost library
BOOST_INCLUDEDIR #location of the include directory of boost
BOOST_LIBRARYDIR #location of the lib directory of boost

*For details, refer to "configure help".
$ bcl2fastq-1.8.4/src/configure --help