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interactivereport / cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.
https://cellxgenevip-ms.bxgenomics.com
MIT License
129 stars 44 forks source link

Issue running cellxgene_VIP #83

Closed curtisd0886 closed 1 year ago

curtisd0886 commented 1 year ago

Hello, I am trying to get cellxgene_VIP running, but keep running into an issue at startup. If I run standard CellXgene through a PIP install I have no issues, but if I follow the CellxGene_VIP installation instructions and try to run I get the following error:

Traceback (most recent call last): File "/opt/anaconda3/envs/VIP/bin/cellxgene", line 5, in from server.cli.cli import cli File "/opt/anaconda3/envs/VIP/lib/python3.8/site-packages/server/cli/cli.py", line 4, in from .launch import launch File "/opt/anaconda3/envs/VIP/lib/python3.8/site-packages/server/cli/launch.py", line 12, in from server.app.app import Server File "/opt/anaconda3/envs/VIP/lib/python3.8/site-packages/server/app/app.py", line 461, in from server.app.VIPInterface import route File "/opt/anaconda3/envs/VIP/lib/python3.8/site-packages/server/app/VIPInterface.py", line 38, in import server.common.compute.diffexp_generic as diffDefault ModuleNotFoundError: No module named 'server.common.compute'

Any Idea what could be causing this? As far as I can tell there were no errors during the installation process. Thanks for your help.

alexlenail commented 1 year ago

+1 same issue

alexlenail commented 1 year ago

It's this line:

https://github.com/interactivereport/cellxgene_VIP/blob/f449f2e018622a87fc9bb208e2c7b9aad668a6fe/VIPInterface.py#L38

Trying to import this module:

https://github.com/chanzuckerberg/cellxgene/blob/main/server/common/compute/diffexp_generic.py

suggesting cellxgene is not installed, or getting being clobbered by something else

z5ouyang commented 1 year ago

@curtisd0886 & @alexlenail Is this the new installation with cellxgene v1.1.1? I did a fresh install without any issues.

z5ouyang commented 1 year ago

cellxgene v1 did a major change from previous version of how their methods could be called. Please reinstall/update the VIP accordingly if you would like to use cellxgene V1. Thanks! Please reopen if the issue still exists.