Running the code given by developer as an example generates the error!

[Xiao-Zhong]

Dear the developers or other users,

Please take a look at the issue below (R version 4.4.0). Any suggestions are very welcome. Or Confirming antigen.garnish doesn't work nowadays is also very helpful! If that, I wouldn't waste too much time here, just because our legacy pipeline uses antigen.garnish. Thanks Thanks Thanks!

[Xiao-Zhong]

[andrewrech]

Please use the docker container.

[Xiao-Zhong]

Thank you, Andrew! Unfortunately, our HPC doesn't have Docker and we as users don't have permission to install it there.

[andrewrech]

This software has a brittle and complex dependency stack. We supply a Docker container to try to lock these things down. There are too many potential HPC deployments for me to support each, but if there is an issue with the Docker container, I am happy to fix it.

I understand not all HPCs support Docker; however, this software is not particularly computationally intensive, and you could run the software using Docker on almost any Mac, Windows, or Linux system you have admin access to, such as a laptop or personal workstation.

[Xiao-Zhong]

OK. I see. May I ask if it's possible to install antigen.garnish via Conda? Conda is allowed on our HPC.

If not, I'll have to run sequencing data processing, mapping and variant calling on the HPC, and then run antigen.garnish for the variants with Docker on my Mac as suggested. Not perfect, but looks good! Thank you!