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apcamargo / genomad

geNomad: Identification of mobile genetic elements
https://portal.nersc.gov/genomad/
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download database manually #1

Closed Thexiyang closed 1 year ago

Thexiyang commented 1 year ago

Is it possible to download database manually instead of genomad download-database? Thanks!

apcamargo commented 1 year ago

Sure! Right now the link is https://portal.nersc.gov/genomad/__data__/genomad_db_v1.0.tar.gz

However I will release a new version really soon with a few additional markers and hallmark information for viral markers. With the download-database command you will always get the latest version of the database (as long as it is compatible with your version of geNomad).

Thexiyang commented 1 year ago

Does it mean I can directly use the db file after unzip? Thanks

apcamargo commented 1 year ago

Yes. The download-database basically checks the latest version of the database, downloads it, and them extracts. You can do that manually if you want.

apcamargo commented 1 year ago

I'll close this issue. Let me know if you got any other questions!

jzrapp commented 1 year ago

Hi @apcamargo! I would like to follow up on this: When I download the db manually and the run the end-to-end command, I get an error right away, because genomad_db/version.txt is missing. When I try to download via download-database it seems like the process is just stalling and nothing happens.

Could you help with that? Thanks so much!

jzrapp commented 1 year ago

Hi again, sorry, I think I realized what the issue was: I downloaded all 4 files from zenodo and kept them in a directory that I named genomad_db. Instead of pointing to the specific genomad_db_v1.1, I pointed to the directory with the 4 files. Sorry about that!

apcamargo commented 1 year ago

No problem :)