Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

[QUESTION] What is the expected format for the --gene-sets-file command? #2666

Open
timothevanmeter opened this issue Mar 25, 2024 · 0 comments
Labels
question request for help/clarification

Comments

@timothevanmeter
Copy link

Hello,

I am trying to import a set of genes in cellxgene at launch time using the --gene-sets-file command, but I always get the following error message:
Error: Unable to read genesets CSV file: Gene set CSV file missing the required column header.

The whole launch command I am using is:
./cellxgene launch --gene-sets-file genes.csv nathans_30dims_k40_res0.2_analysed_assigned.h5ad -p 5005

The cellxgene version is cellxgene v1.1.2 and the launch works perfectly fine without the import with
./cellxgene launch nathans_30dims_k40_res0.2_analysed_assigned.h5ad -p 5005
The GUI is accessible at localhost:5005 withtout any problem.

The genes.csv file looks like this:
Rho,Epha7,Gnat1

I tried a bunch of different formats for the csv file without any success.
Is there an expected format that will work for the import?

Thank you in advance for your consideration.

@timothevanmeter timothevanmeter added the question request for help/clarification label Mar 25, 2024
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
question request for help/clarification
Projects
None yet
Development

No branches or pull requests

1 participant