[BUG]rgi database --version N/A

[alex-trist]

I recently installed rgi using mamba in a new environment. Then I tried wget https://card.mcmaster.ca/latest/data tar -xvf data ./card.json rgi load -i Data_Bases/CARD/card.json

but when I check the version with rgi database --version

result is N/A

Same applies with the --local flag

Any thoughts.

Thanks!

CARD Version 2.3.8

RGI version 6.0.3

Expected behavior Display 2.3.8 in database version

[raphenya]

@alex-trist Thank you! I will fix it. Cheers.

[jduquez]

Hi @raphenya same error! any progress?

cheers

[raphenya]

@jduquez I haven't fixed this yet, but soon. Cheers.

[b-tierney]

Hi -- I think I'm bumping into the same issue, but it's with the wildcard database. I'm trying to figure out what the current release number is for the loading process as I setup RGI. Can you point to where that info is found? I see card is 3.2.8, but don't see metadata for wildcard.

eg

rgi wildcard_annotation -i wildcard --card_json card.json -v ??? > wildcard_annotation.log 2>&1

[raphenya]

@b-tierney If you want to see loaded database use the following:

card canonical (i.e loaded only card.json)

rgi database --version

Wildcard (loaded everything e.g rgi auto_load)

rgi database --version --all

[b-tierney]

Thank you —but don’t you have to specify the database when you load? Eg the above command requires you to specify the database, and as far as I can tell it needs to be run before rgi database —version?

It seems circular, but maybe I’m misunderstanding something.

On Jan 5, 2024, at 12:05 PM, amos @.***> wrote:

@b-tierney https://github.com/b-tierney If you want to see loaded database use the following:

card canonical (i.e loaded only card.json)

rgi database --version

Wildcard (loaded everything e.g rgi auto_load)

rgi database --version --all

— Reply to this email directly, view it on GitHub https://github.com/arpcard/rgi/issues/258#issuecomment-1878991436, or unsubscribe https://github.com/notifications/unsubscribe-auth/AE2N6PV2PQGFS7PHWFTJBTLYNAXE5AVCNFSM6AAAAAA7RV5XMGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQNZYHE4TCNBTGY. You are receiving this because you were mentioned.

[raphenya]

@b-tierney we wanted to be able to add each database separately. It is best to use rgi auto_load to get the latest dbs.

[sciguy]

I'm getting the same result (NA) when checking the database version from the latest docker:

docker run -it quay.io/biocontainers/rgi:6.0.3--pyha8f3691_1 rgi database -v
# => N/A