can't download reference genome/annotation

[shoy91]

Hi!

I'm trying to run transvar config --download_ref --refversion hg19 and transvar config --download_anno --refversion hg19. It will create a download folder (.transvar.download) in my home directory but nothing is in it. I've also tried to change the transvar download directory by specifying a path to it in my env variable like you all had suggested (ie. export TRANSVAR_DOWNLOAD_DIR=/diskmnt/Software/bin/transvar.download). Nothing happens and it seems to still create a folder in my home directory. Can you help me with this?

Thanks!
Sohini

[shoy91]

I figured it out! nvm!

[Anita S. Bowman]

Hi @shoy91 , what did you do to get it to work?

[Wanding Zhou - Bioinformatics]

Hi @NitaH0321 see if you can access http://transvar.info/transvar_user/annotations/ This is currently where annotations were retrieved.

[jianl]

Hi @zwdzwd, do you by any chance have the CCDS transvardb files available for hg38 please?

[Matteo Ferla]

Also for me the config seems to be unable to download the files (Mac OS 10.15). Looking at the config.py I see the above URL (transvar.info) is depracated and that http://zwdzwd.io/ is used. However, http://zwdzwd.io/transvar_user/annotations/uniprot.idmapping.txt.gz.idx or any of the URLs gives a status 404 response. Switching on the SSL layer (https) does the same. So if the URL has changed, what is it? Thanks

[Linhe Huo]

transvar.info is down too. Does anyone know an alternative download site?

[Matteo Ferla]

I apologise that it's rather ungracious mentioning other tools, but as the databases are down, I ought to mention that I ended up using Backlocated —java based though.