Reference files missing from server

[joe-albert]

Hi,

We have a setup pipeline for transvar where we run the command: transvar config --download_ref --refversion hg38

During this step we get the following warning: [download] warning: file not available: https://zhouserver.research.chop.edu/TransVar/annotations//hg38.fa or target directory not found [download] warning: file not available: https://zhouserver.research.chop.edu/TransVar/annotations//hg38.fa.fai or target directory not found

When I check the server index these files are indeed missing. Am I missing something or is there a way to run the transvar pipeline without these files? If it matters, running using python@3.7

Thanks for any help you can offer!

[joe-albert]

Bioinformatics isn't my domain of expertise so maybe this was painfully obvious to anyone who might look at this issue and isn't really a problem.

That being said, I have figured out how to get these files from other sources: hg38.fa can be found from ucsc and the hg38.fa.fai file apparently is generated from the .fa file --> On a mac:

brew install samtools
samtools faidx hg38.fa               // to generate the fa.fai file

// then placed both of these in the transvar.download folder

I'm going to leave this open since it seems like the tool would prevent us having to do this if the files were being hosted still. But also, I understand if it's something SUPER simple and it should be closed :)

Thanks!