Use giraffe in vg

Question

[Michal]

I am trying to run "vg autoindex --workflow giraffe" and get the reply: "giraffe indexing not yet implemented" Why?

[biofalconch]

What version of vg are you using? They have that exact line in their documentation so I think it might be an older version you are using. Also I just noticed that your tags has a typo (vg. insteead of just vg), could you (or a person with the right permissions) change it so that it might catch the eye of the devs? :)

[Michal]

my version is: vg version v1.30.0 "Carentino" Is it an old one? (I downloaded it last week...) How can I upadate my version?

[Jordan M Eizenga]

Yeah, that's over 2 years old. The current version can be downloaded from the GitHub page: https://github.com/vgteam/vg/releases

[Michal]

I downloaded the new version (vg-v1.49.0) and I can see the folder in my directory but the vg command still work with the old version (when I ask the version I get 1.3.00.0 and when I try to use giraffe I get the response that giraffe is not yet implemented). How can I activate the new version?

[Jordan M Eizenga]

My guess is that this is an issue with your Unix path. You can try which vg to check the location of the vg binary that's being picked up. I'd recommend deleting the old version.

[colindaven]

You can also check the commands from this issue for comparison in addition to biofalconch's suggestion: vg tools, I ran vg autoindex -w giraffe and use splited vcf file (multi vcf file) then index registry error is happened

[Jordan M Eizenga]

Updating the VG version should resolve this. Giraffe autoindexing has been implemented since February of 2021.