Help with Installing CellViT via GitHub

[Mattia1311]

I’m reaching out because I’m encountering issues while trying to install the CellViT package from GitHub. I’m not an expert in IT or bioinformatics, but as suggested in your guidelines, I cloned the GitHub repository onto our institution’s HPC, placing it in a specific folder. Then, following your instructions, I attempted to create the Conda environment by running the following command:

conda env create -n CellViT_4 -p /storage/data/GS/sw/mtonani/ubi9/9.2/miniconda3/py311_23.9.0-0/ -f environment.yml

The problem is that the installation process is taking an unusually long time (it's been running for over 3 hours and still hasn’t finished). I suspect there might be some issues I’m unable to resolve on my own.

Could you please assist me?

Thank you in advance.

Best regards,
Mattia Tonani

[Mattia1311]

I have an update: it gave me error. The following is the error I had:

note: This error originates from a subprocess, and is likely not a problem with pip.
error: legacy-install-failure

× Encountered error while trying to install package.
╰─> openslide_python

note: This is an issue with the package mentioned above, not pip.
hint: See above for output from the failure.
WARNING: There was an error checking the latest version of pip.
failed

CondaEnvException: Pip failed

I also tried to install openslide_python version 1.2.0 (the one suggested in the environment.yml) alone with the other packages but it raised me error.

[kountaydwivedi]

I have an update: it gave me error. The following is the error I had:

note: This error originates from a subprocess, and is likely not a problem with pip. error: legacy-install-failure

× Encountered error while trying to install package. ╰─> openslide_python

note: This is an issue with the package mentioned above, not pip. hint: See above for output from the failure. WARNING: There was an error checking the latest version of pip. failed

CondaEnvException: Pip failed

I also tried to install openslide_python version 1.2.0 (the one suggested in the environment.yml) alone with the other packages but it raised me error.

Facing the same issue.