[BUG] Can not start cellxgene about cellxgene

[MaximilianLombardo]

Hey @pati-ni, thanks for the report! Could you try reproducing the error with one of the datasets downloaded from our data portal?

I was able to reproduce an error (albeit a different one than you encountered) with the PBMC3K object, but was able to get CELLxGENE to successfully launch when using a dataset (.h5ad) downloaded from the data portal - I'd like to check if the error you are encountering is a dataset issue rather than a CELLxGENE issue

Also, can you let us know what version of CELLxGENE you are running?

[pati-ni]

Hi MaximilianLombardo, thank you for your quick reply. cellxgene is v1.1.2. Numpy is v1.22. As you suggested, I downloaded the "scRNA-seq data - lymphatic cells" from the portal and I got exactly the same behaviour running it from passing the file locally. I do not think the file is being opened in the first place because the error is almost instant whereas I would expect the launch to lag until the file is downloaded. Is there a specific dependency that my environment is missing?

[MaximilianLombardo]

Ok thanks for the info - yea the versions of CELLxGENE and Numpy look ok - have you tried installing CELLxGENE in a fresh conda environment?

[pati-ni]

This was on a new fresh conda environment. I actually just fixed it. The culprit, was a defunct pandas package. Not sure why.. Pandas work fine in different environments. I installed the latest version from conda and the app launched with no problems. Thanks for the support

[MaximilianLombardo]

ahh understand, thanks for letting us know you've been able to resolve the issue!