Unable to run download_reference.sh on Mac

Illumina / GTCtoVCF

Script to convert GTC/BPM files to VCF

Apache License 2.0

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Unable to run download_reference.sh on Mac #55

Closed biying-orig3n closed 4 years ago

biying-orig3n commented 4 years ago

I tried to build suitable whole genome FASTA files can be built with the download_reference.sh script on macOS Mojave: ./download_reference.sh output-37.fa 37

I got this error: readlink: illegal option -- f usage: readlink [-n] [file ...] usage: dirname path

Does anyone know how to fix it? Thanks in advance!

jjzieve commented 4 years ago

Hi, can you try this PR branch? https://github.com/Illumina/GTCtoVCF/pull/39

biying-orig3n commented 4 years ago

Thank you, @jjzieve ! PR#39 works. Before running this script, I need to get realpath on Mac: brew install coreutils Also need to install samtools: http://www.htslib.org/download/

jjzieve commented 4 years ago

Should be fixed with PR #39