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2.9 years ago
ddraki2008
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0
I'm trying to decide if to upgrade from High Sierra to Catalina or Big Sur. For standard NGS data analysis what OS system between High Sierra, Catalina, and Big Sur gives fewer errors for installing with Conda and running typical tools for RNAseq, WGS, Genome analysis, ChipSeq, and various other NGS data analysis?
A newer version is probably better most of the time, but I doubt it will make much of a difference in your case. The main changes between versions are on the fancy UI functionalities, while the unix core (Darwin) shouldn't be that different. Have a look at the list of changes between versions, and see if there is something that could impact your pipelines.
Thank you for your input. So far on High Sierra, I was able to install without problems by using either conda either brew main bioinformatics tools as samtools, picard, bcftools, pangolin, etc. However, it was a headache to install for instance MySQL (not bioinformatics related) on HS, and I understood that it would have been much easier to do this on Catalina and I assume Big Sur as well. Now I have problems installing java for GATK4 installation. when I type java -version I get Error: A JNI error has occurred, please check your installation and try again Might be easier to install on Big Sur? Besides, I also get the message that macOS HS is not supported by mac anymore, which in time might become a problem. In any case, I wouldn't like to solve java installation issues for instance by upgrading to Big Sur and not be able to install instead others bioinformatics tools. So, my question is really if you heard of any specific issues in installing various bioinformatics tools on Big Sur. On Catalina, I saw that were some issues with samtools.
If you have any 32-bit apps you must use then they are not going to work with Catalina onwards. Keep that in mind. Otherwise there should not be much of a problem using Big Sur for normal work.
yes, thank you for your answer! I read about the 32 bit...however, I'm not sure how many bioinformatics tools these days are 32 bits, therefore might be not a concern for me:)