The chip-set-pipeline2 fails because the pipeline is unable to merge the fastq.gz files using cat. I have run it several times - on my Mac desktop and the pipeline always fails at the same point. I am a bit of a newbie at this type of analysis and am using
a Mac OS Big Sur
with conda 4.9.2
Pipeline version v1.6.1 (download da few days ago)
with caper 1.4.2
I tried adding coreutils to my path, /usr/local/opt/coreutils/libexec/gnubin but that didn't work either.
Is there a relatively simple workaround for the zcat function that I can utilise to allow me to use the pipeline?
The chip-set-pipeline2 fails because the pipeline is unable to merge the fastq.gz files using cat. I have run it several times - on my Mac desktop and the pipeline always fails at the same point. I am a bit of a newbie at this type of analysis and am using
a Mac OS Big Sur with conda 4.9.2 Pipeline version v1.6.1 (download da few days ago) with caper 1.4.2
I tried adding coreutils to my path, /usr/local/opt/coreutils/libexec/gnubin but that didn't work either.
Is there a relatively simple workaround for the zcat function that I can utilise to allow me to use the pipeline?
Many thanks,
Debbie