Question: What should I do if I am having trouble installing bcl2fastq?
Answer: Illumina does not provide standalone bcl2fastq or bcl-convert binaries. They can be compiled statically or using shared libraries.
They are also available as rpm packages. Some of our customers have had luck extracting the executable from the rpm using the following commands:
After downloading bcl2fastq or bcl-convert rpm file from Illumina and unzipping, run this:
rpm2cpio ./bcl2fastq2-v2.20.0.422-Linux-x86_64.rpm | cpio -idmv
or
rpm2cpio ./bcl-convert-3.9.3-2.el7.x86_64.rpm | cpio -idmv
The bcl2fastq executable will be found in the current directory here:
./usr/local/bin/bcl2fastq
The bcl-convert executable will be found in the current directory here:
./bclconvert_v3.9.3/usr/bin/bcl-convert
Please note that bcl2fastq and bcl-convert demultiplexing software tools are not developed by 10x Genomics. While this information and guidance is accurate to the best of our knowledge, we can't guarantee that these instructions are completely up-to-date or that Illumina has not changed bcl2fastq or bcl-convert distribution since this article was written.
If you notice any inaccuracies, feel free to let us know by contacting support@10xgenomics.com.
If you need further assistance with installing bcl2fastq or bcl-convert, please contact Illumina support directly at techsupport@illumina.com or at the Illumina support page.