how to run_params from an outside of the repo

[alxndrkalinin]

I wanted to define a relative data_path in a config to make it user-independent (i.e. avoid overriding results folder and configs on Github), but seems like some paths in evalzoo are defined locally.

E.g., defining data_path: "../1.load/output" and trying to run from another repo gives following:

setwd("matric")
source("run_param.R")
setwd("../../position-effect-correction/2.evalzoo")
run_param("params/params_orf_group.yaml")

gives

Error in abs_path(input) : 
  The file '0.knit-notebooks.Rmd' does not exist.
In addition: Warning message:
In normalizePath(x, winslash = winslash, mustWork = must_work) :
  path[1]="0.knit-notebooks.Rmd": No such file or directory

I was able to make it work with data_path: "../../position-effect-correction/1.load/output" and

run_param("../../position-effect-correction/2.evalzoo/params/params_orf_group.yaml", results_root_dir = "../../position-effect-correction/2.evalzoo/results/")

however, it assumes both repos being located in the same directory, so doesn't fully address issues above.

[shntnu]

Oops – I certainly put in no effort into this being more than barely usable :D

both repos being located in the same directory,

Can you clarify what you mean by "both repos"?

[alxndrkalinin]

Oh sorry, I just meant if your evalzoo and position-effect-correction were not checked out to the same directory, then data_path: "../../position-effect-correction/1.load/output" will be incorrect, because it's a relative path from a working directory (that has to be inside evalzoo) to a file inside position-effect-correction.

Basically, when you create a new config for calculating metrics on a dataset, data_path inside this config always has to account for the relative location of of this dataset to evalzoo.

Does this make sense?

[shntnu]

Ah got it

So in this param file, you wish you could have specified

https://github.com/broadinstitute/position-effect-correction/blob/cda9e242aebea8031bd01a5a358a2c3507f9f3cb/2.evalzoo/params/params_orf_group.yaml#LL3C11-L3C11

as

data_path: "../1.load/output"

(Now I understand your first comment)

[alxndrkalinin]

Yep, exactly. And I think it comes down to being able to run run_params from outside of evalzoo/matric.

[shntnu]

Got it, and that's where the current strategy of using notebooks as functions gets a bit messy :D I'll keep this open for now and see if there's an easy fix