[GENERAL] Wrong version of hv_rapidCNS2/bin/methylation_classification_nanodx_v0.2.R

[jasteen]

📝 Description

Error with versioning of methylation classification scripts.

full trace.

ERROR:robin.subpages.RandomForest_object:R script not found at: /Users/jste0021/Documents/scripts/robin/src/robin/submodules/hv_rapidCNS2/bin/methylation_classification_nanodx_v0.2.R ERROR:robin.subpages.RandomForest_object:Error in run_rcns2: R script not found: /Users/jste0021/Documents/scripts/robin/src/robin/submodules/hv_rapidCNS2/bin/methylation_classification_nanodx_v0.2.R Traceback (most recent call last): File "/Users/jste0021/Documents/scripts/robin/src/robin/subpages/RandomForest_object.py", line 410, in forest_bam_background_work await run.cpu_bound( File "/Users/jste0021/miniconda3/envs/robin_0_3/lib/python3.9/site-packages/nicegui/run.py", line 82, in cpu_bound return await _run(process_pool, safe_callback, callback, *args, **kwargs) File "/Users/jste0021/miniconda3/envs/robin_0_3/lib/python3.9/site-packages/nicegui/run.py", line 62, in _run return await loop.run_in_executor(executor, partial(callback, *args, **kwargs)) nicegui.run.SubprocessException: Exception in subprocess: Type: FileNotFoundError Message: R script not found: /Users/jste0021/Documents/scripts/robin/src/robin/submodules/hv_rapidCNS2/bin/methylation_classification_nanodx_v0.2.R Traceback (most recent call last): File "/Users/jste0021/miniconda3/envs/robin_0_3/lib/python3.9/site-packages/nicegui/run.py", line 51, in safe_callback return callback(*args, **kwargs) File "/Users/jste0021/Documents/scripts/robin/src/robin/subpages/RandomForest_object.py", line 83, in run_rcns2 raise FileNotFoundError(f"R script not found: {r_script_path}") FileNotFoundError: R script not found: /Users/jste0021/Documents/scripts/robin/src/robin/submodules/hv_rapidCNS2/bin/methylation_classification_nanodx_v0.2.R

❓ Context

Running the dev branch as described elsewhere in the issues here. everything else seems to work and give results, however the methylation classification obviously fails.
i've looked everywhere for the 0.2 version of that script but cant find one, and indeed notice that the fork of rapidCNS2 that you use is now archived and rebranded as "SCARLET"

Expected outcome?

Hopefully i'm just using an outdated version, or there are complete versions of the requred script somewhere I cant see them.

further info

running on Macbook PRO, apple silicone

[mattloose]

Please run:

git submodule update --init --recursive

And you should find the file will appear...