Closed rdmorin closed 1 year ago
This file is on master, e.g.: https://github.com/morinlab/gambl/blob/master/data/metadata/BLGSP--DLBCL-case-set.tsv
I think what is missing is that get_gambl_metadata()
should use the config::get()
and construct the path to this (and other) files like we do in other functions rather than have it hardcoded. Similar would need to be done also for case sets BL-DLBCL-manuscript-HTMCP
and FL-DLBCL-all
.
I am working on update to other GAMBLR functions, and can fix this bug there
Some of the sample sets that can be accessed with get_gambl_metadata cause the function to break if run off-site. This is because files it's using do not exist in the repo or the path is specified wrong. For example:
All files that GAMBLR loads must be either in the gambl repo (with the path specified properly using the relative path and config) or, in rare cases, bundled with GAMBLR.