EnvironmentLocationNotFound error for installation on HPC with sudo rights

[joao1980]

Thanks for the tool. I am currently trying to test it. I am working on a HPC without sudo rights. Having said that, I managed to install all modules by setting my conda environments to a specific folder. However, when I try to run , e.g., annotate, it fails.

EnvironmentLocationNotFound: Not a conda environment: /xxx/global/software/skylake/software/Mamba/23.3.1-1/envs/VEBA-annotate_env

Traceback (most recent call last): File "/home/xxx/.conda/envs/VEBA/bin/annotate.py", line 10, in from genopype import * ModuleNotFoundError: No module named 'genopype'

I'm guessing this will happen no matter the module. How can I fix this? Thanks in advance. Cheers, Joao

[jolespin]

Looks like the environment creation failed. I've seen similar situations happen on lab-specific HPCs that aren't managed by an institute.

A few questions:

• Do you have SLURM/SunGridEngine on here or do you run everything on the head node?
• How much memory was allocated during the installation?
• Can you provide the error message?

If you have sudo rights then you might want to consider using the Docker workflow.

https://github.com/jolespin/veba/blob/main/walkthroughs/docs/adapting_commands_for_docker.md https://www.youtube.com/watch?v=3aFV-3rsJ5w&t

[jolespin]

Feel free to reopen if this issue persists