Question: What should I do if I am having trouble installing bcl2fastq?
Answer: Illumina does not provide a standalone bcl2fastq binary. It can be compiled statically or using shared libraries.
It is also available as an rpm package. Some of our customers have had luck extracting the executable from the rpm using the following commands:
# Download bcl2fastq rpm from Illumina and unzip
rpm2cpio ./bcl2fastq2-v2.20.0.422-Linux-x86_64.rpm | cpio -idmv
The bcl2fastq executable will be found in the current directory at ./usr/local/bin/bcl2fastq
Please note that bcl2fastq is not developed by 10x Genomics, so while this information and guidance is accurate to the best of our knowledge, we can't guarantee that is completely up-to-date or that Illumina has not changed bcl2fastq 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, please contact Illumina support directly at techsupport@illumina.com or at the Illumina support page.