cellxgene_VIP icon indicating copy to clipboard operation
cellxgene_VIP copied to clipboard

Published 20 hours ago • verified publisher icon interactivereport

Plugins are not available for the new cellxgene version 1.0.1

Open pkhoueiry opened this issue 2 years ago • 4 comments

@z5ouyang Upon upgrading cellxgene to version 1.0.1, the plugins are not available anymore!

pkhoueiry avatar Jun 02 '22 10:06 pkhoueiry

I have the same issue. After installation there's a prompt to update to version 1.0.1 with pip install. After that the VIP panel disappeared. @interactivereport @z5ouyang any suggestions please?

JialiUMassWengLab avatar Jun 27 '22 18:06 JialiUMassWengLab

After communicating with the developers, version 1.0.1 is not ready yet. So users should refrain from upgrading to v1.0.1 for now. Additionally it is advisable to use the Scanpy contained within the VIP virtual environment to generate the .h5ad files. I used a later version (v1.9.1) and cellxgene won't recognize the .h5ad file generated that way.

JialiUMassWengLab avatar Jul 15 '22 00:07 JialiUMassWengLab

Same issue but our lab has just started self-hosting using cellxgene 1.0.1 for the past few months. We want to expand to use cellxgene VIP but are unsure whether to downgrade and risk issues with cellxgene-gateway and cellxgene by going back to the previous version, or wait for the new update to cellxgene VIP

Dane-Z avatar Aug 22 '22 14:08 Dane-Z

Some datasets fail to launch on cellxgene-VIP using s3 urls as well. Although it has to with cellxgene version 0.16.8 and not VIP per se, but this issue has been fixed with cellxgene version >=1.0.1, so I'm curious if there are any plans to update VIP

tjneu avatar Sep 28 '22 15:09 tjneu

If you run "config.sh" again in your conda env. will be using cellxgene v1.1.1

z5ouyang avatar Oct 28 '22 06:10 z5ouyang