Frequently asked questions

If you cannot find the answer to your problem here, please post it as an issue on GitHub.

How do I fix crashes?

Cellxgene Gateway - Process Error

Crashed sessions often display the error Cellxgene Gateway - Process Error. These crashes can have different causes, which can be differentiated by the text next to “Stderr”. Find the question most closely related to your Stderr text.

Stderr contains: Usage: cellgene launch <options> <path to data file> Error: Got unexpected extra arguments

This error often means that there are spaces in the name of the .h5ad file or in one of the folders within which it is contained. Remove these spaces and see if this solves the problem.

Stderr ends: PrepareError: No valid layout data.

This often means that there is no UMAP or PCA (or other valid) dimensionality reduction in your h5ad file. You must first compute one: Portable-CELLxGENE does not compute these itself, but simply displays existing ones.

On Windows, Portable-CELLxGENE is prevented from launching

Windows requires a significant number of users before allowing software to run without a warning. Before this number is reached, it is likely to display a warning the first time it is run. See the Windows installation instructions for how to fix this.

On Windows, Python is prevented from launching

The Windows firewall can prevent Python from running. You can allow its access from the pop-up. You may need to restart CELLxGENE for this to take effect.

How can I cite Portable-CELLxGENE?

See here.