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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
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timestamp file missing / permissions? #107

Closed bobermayer closed 5 months ago

bobermayer commented 5 months ago

Hi,

this is really great. I managed to adapt and use the Dockerfile (#102), but I'm getting errors in the VIP that seem unrelated

when running cellxgene like so

docker run -it -p 8050:8050 cellxgene_vip_slim launch --host 0.0.0.0 --port 8050 --disable-annotations -var feature_name https://datasets.cellxgene.cziscience.com/676c47a4-bd2c-4f09-82cb-2dfcd54be04a.h5ad

I can see and use the cellxgene interface just fine, and also start the VIP. but whenever I actually try to get a plot, I'm getting

ERROR @server: Traceback (most recent call last):
FileNotFoundError: [Errno 2] No such file or directory: 'https:/datasets.cellxgene.cziscience.com/676c47a4-bd2c-4f09-82cb-2dfcd54be04a.timestamp'

same thing happened with local datasets mounted read-write, with/without sudo ...

I noticed a typo (it says https:/datasets.cellxgene...) not sure if that's causing the issue.

the timestamp seems to be generated here I tried adding the timestamp myself for a local h5ad file, but that didn't help either:

ERROR @server: Traceback (most recent call last):
PermissionError: [Errno 13] Permission denied: 'data/filtered_results_prog.timestamp'

help greatly appreciated! thanks!

bobermayer commented 5 months ago

ok so I had to comment out line 62 to avoid setting a timestamp. now it works very well.