RECOVAR/pipeline file not found

[ncoudray]

Hi - Thanks for sharing the code and for detailed instructions.
We are using recovar via SBGrid installation and use the "python.recovar" command (looks like it's replacing the "recovar" one). When we try to run it from the folder when the pkl and particle stacks were saved, we get this error message:

/vast/arch/sbgrid//x86_64-linux//recovar/20250226/.pixi/envs/default/bin/python: can't open file '/my_directory/RECOVAR/pipeline': [Errno 2] No such file or directory

Do you have any idea what could happen there?

Thanks,
Best,
Nicolas

[cherre]

Hello,

I installed the version of RECOVAR from the Main branch on 2025 Feb 26. recovar didn't exist in that version of the code. I am updating the SBGRID install to use the latest version and it seems that the run_test_dataset is missing. I used run_test_dataset.py to verify my previous installation. thanks -- carol

[ma-gilles]

Hi Carol and Nicolas,

It seems that you have figured it out yourself, but let me know if you still have questions!

If others are running into this issue:

The scripts (pipeline, run_test_dataset, etc) are now in recovar/commands

But if you pip install the package as in the new instructions, you can run them by doing:

conda activate recovar
recovar pipeline (rest of arguments)

Note: no need to use .py if you run them this way, or to point to the directory where pipeline.py is.

Thank you for giving it a try!

Best,
Marc