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KarchinLab / open-cravat

A modular annotation tool for genomic variants
MIT License
113 stars 27 forks source link

onkokb module failed because not in store #137

Closed lmanchon closed 1 year ago

lmanchon commented 1 year ago

oc module install onkokb No modules to install found

oc module info onkokb NOT IN STORE NOT INSTALLED

How to install onkokb module ?

RachelKarchin commented 1 year ago

The command should work but there is a "c" in oncokb

Try this: oc module install oncokb

lmanchon commented 1 year ago

sorry i have misspelled the word, i have installed oncokb with oc module install oncokb, iinstallation works fine, but in annotation the corresponding column of oncokb still empty.

kmoad commented 1 year ago

Oncokb needs an api token provisioned by the user. OpenCRAVAT cannot re-distribute the token. There are more details on the oncokb module panel in the store.

In brief, get a token from https://api.oncokb.org/oncokb-website/api. Then put it in a subfolder of the oc modules directory. To find the location of your modules directory, run oc config md. Then put the token in to <md>/annotators/oncokb/data/token.txt

Let us know if this works.

lmanchon commented 1 year ago

it seems token isn't free for all users.

kmoad commented 1 year ago

Yes, I believe it's free for academic users only. Sorry that we couldn't be more help here.