morinlab / GAMBLR

Set of standardized functions to operate with genomic data
https://morinlab.github.io/GAMBLR/
MIT License
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get_gambl_metadata relies on files that aren't in the repo #127

Closed rdmorin closed 1 year ago

rdmorin commented 1 year ago

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:

get_gambl_metadata(case_set="BL-DLBCL-manuscript")
Error in data.table::fread("/projects/rmorin/projects/gambl-repos/gambl-kdreval/data/metadata/BLGSP--DLBCL-case-set.tsv") :                                                                               
  File '/projects/rmorin/projects/gambl-repos/gambl-kdreval/data/metadata/BLGSP--DLBCL-case-set.tsv' does not exist or is non-readable. getwd()=='/Users/rmorin/git/GAMBLR'

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.

Kdreval commented 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