IGS/gEAR

Visualizing marker genes return an error

Closed this issue · 3 comments

beamilon commented

@adkinsrs
@jorvis
I tried to visualize marker genes from the sc workbench (tried several datasets) and it returns an error. I also tried to capitalize the gene names and the error is the same. The problem is just for the genes that are typed in. The visualization works perfectly for genes selected in the table.
Below is an example with the P1, mouse, scRNA-seq, cochlear epithelium (Kelley).

image

adkinsrs commented

Testing is going to be interesting here.... the production server uses scanpy 1.7.2 and the devel server (and my local one) use scanpy 1.8.2, and the QC-to-mito server-side script is throwing an error when using the later version. So I need to resolve that to get to the right workbench step, or backport my scanpy version which requires a rebuild of my docker image.

EDIT - I believe it is the difference in numpy (1.21.5 vs 1.24.0) that is causing my issue

EDIT2 - Issue is resolved by upgrading numpy to 1.26.0 - Back to our regularly scheduled troubleshooting

adkinsrs commented

Made a direct change on the production server. @beamilon can you verify it works now?

beamilon commented

@adkinsrs
It's working perfectly. Thanks.