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TheJacksonLaboratory / LIRICAL

LIkelihood Ratio Interpretation of Clinical AbnormaLities
https://thejacksonlaboratory.github.io/LIRICAL/stable
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lirical fails to download necessary data files #665

Open AO33 opened 4 days ago

AO33 commented 4 days ago

After I download the latest release of lirical and run the following command, I get an error

java -jar lirical-cli-2.0.2.jar download

"ftp://ftp.ebi.ac.uk/pub/databases/genenames/hgnc/tsv/hgnc_complete_set.txt" Link is no longer available... Download links need updating maybe?

ielis commented 4 days ago

Hi @AO33, thank you for pointing the issue out. The link is indeed dead and should be changed to

https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt

We will work on updating the link.

In the meantime, please download the file manually from the abovementioned link and put it into LIRICAL's data directory before running the download command. The command will proceed with downloading the remaining files if it sees that the hgnc_complete_set.txt file is already downloaded.

AO33 commented 4 days ago

Thanks! Will do

AO33 commented 4 days ago

Would it be possible to have the release download the latest version of refseq variant information? A frameshift variant found in NM_001267044.1 has been supressed by refseq, but shows up in our data. (maybe this is a different issue altogether)