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cBioPortal / cbioportal

cBioPortal for Cancer Genomics
https://cbioportal.org
GNU Affero General Public License v3.0
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configure `cbioportalR::set_cbioportal_db` for private authentication #10786

Closed jgarces02 closed 4 months ago

jgarces02 commented 4 months ago

Hi,

The link to the tutorial (it should be here) for configuring a private authentication in cbioportalR is broken, and I'm having some problems connecting to the internal MSKCC cBioportal. Thanks!

> library(cbioportalR)
> set_cbioportal_db(db = "mskcc.cbioportal.org")
Error in `value[[3L]]()`:
! Not able to connect to "mskcc.cbioportal.org/api"
Run `rlang::last_trace()` to see where the error occurred.
jgarces02 commented 4 months ago

Solved, sorry for the dumb question (although the link is still broken).

> library(cbioportalR)
> Sys.setenv(CBIOPORTAL_TOKEN= "...")
> set_cbioportal_db(db = "msk")