Installation issue

[nachonacho2]

Hi,
I am trying to install TRACERx-PHLEX in an online linux environment (https://lightning.ai)
I am following the instructions here: https://tracerx-phlex.readthedocs.io/en/main/quickstart.html
I have successfully completed up to step 5 Launch TRACERx-PHLEX by calling the runPHLEX.sh script from the command line:
./runPHLEX.sh

I am facing two main issues (ml command not found and remote resources not found), as detailed in the output copied below. Thoughts on how to proceed?

⚡ ~/PHLEX_testing ./runPHLEX.sh
./runPHLEX.sh: line 4: ml: command not found
./runPHLEX.sh: line 5: ml: command not found
./runPHLEX.sh: line 6: ml: command not found

N E X T F L O W ~ version 24.10.2

Pulling TRACERx-PHLEX/deep-imcyto ...
Remote resource not found: https://api.github.com/repos/TRACERx-PHLEX/deep-imcyto/contents/main.nf

N E X T F L O W ~ version 24.10.2

Pulling TRACERx-PHLEX/TYPEx ...
Remote resource not found: https://api.github.com/repos/TRACERx-PHLEX/TYPEx/contents/main.nf

N E X T F L O W ~ version 24.10.2

Pulling TRACERx-PHLEX/Spatial-PHLEX ...
Remote resource not found: https://api.github.com/repos/TRACERx-PHLEX/Spatial-PHLEX/contents/main.nf

[Precancer]

Hello nachonacho2,

You can comment or remove the line(s) with the command ml (module load) and ensure that the required software is installed, ideally using the tested versions. More details about PHLEX setup can be found in the detailed step-by-step guide
https://tracerx-phlex.readthedocs.io/en/main/guides.html or directly on
https://tracerx-phlex.readthedocs.io/en/main/_downloads/6df657397b98fc05f976dbd9b4afa335/ReadTheDocs_Tutorial.pdf

Can you check whether the second issue is still there?

[nachonacho2]

execution_report.txt
Thanks for your help Precancer. I now overcome these issues (following your linked PDF tutorial) but have now encountered a bunch of errors when trying to run the test MCCS workflow. Please see attached the execution report for details of the errors (renamed from .html to .txt to enable uploading here).
Any ideas how to proceed?

[nachonacho2]

Hi, would it be possible for you to make a working demo using a free/accessible resource like lightning.ai or colab?