Issues running with conda
edridgedsouza opened this issue · 3 comments
Spent quite a while trying to debug this after I tried the web tool and got the error message "Error: 🛑 No such file: Healthy_Human_Liver.pkl"
conda create -n celltypist python=3.9
conda activate celltypist
mamba install celltypist -c bioconda -c conda-forge # or, `pip install celltypist`
python
> import celltypist
If I install via conda, then open up python and import celltypist, I get an immediate error due to clashes with unrelated class types in imported libraries. Spent a while trying to hunt down a solution, which led to installing a downgraded version of matplotlib, which caused a different error. Even tried running from a Docker image on Dockerhub to no avail. Played whack-a-mole just trying to get the library to import, when I created a fresh env and installed using pip instead. This time it worked just fine!
I ran this on an aws r5.4xlarge ubuntu instance with only mamba and its dependencies installed in the base conda env. Not sure what the issue is, or if it's a problem specific to my machine, but figured I'd send a message in case the version on conda is somehow running differently than the one on pip.
Hi @edridgedsouza Could you please paste here the full error you're getting?
Regarding the containerized version —Docker image— you can pull the official ones from Quay.io here: https://quay.io/repository/teichlab/celltypist?tab=tags
I'm not sure which images from DockerHub you used, but the ones deescribed in the docs (on quay.io) should be work.
Had a quick look and it seems like it's derived from an upstream package (scanpy) scverse/scanpy#2411
EDIT @edridgedsouza forcing scanpy to the latest version should solve the issue:
mamba install 'scanpy>1.9' celltypist -c bioconda -c conda-forge
Thanks, @prete! I actually pulled from https://hub.docker.com/r/prete/celltypist. It seems the issue you identified is what's behind it.