Error when running docker container about azimuth

[andrewwbutler]

Hi,

Yes, for now a demo dataset is required. We will look into making this optional so it doesn't crash without one but the easiest solution currently is to just specify a demo file (can just be a trivial/dummy dataset to get it running).

[doncarlos999]

Thanks for the super quick response.
Where in the docker run command should I specify the demo dataset?

[andrewwbutler]

You can specify it in the AzimuthApp command. E.g.

docker run -it -p 3838:3838 -v /path/to/reference:/reference-data:ro azimuth R -e "Azimuth::AzimuthApp(reference = '/reference-data', demodataset = 'demo.rds')"

Alternatively, we often use a config file to specify a lot of these kinds of things. You can see examples of those in the azimuth-references repo --- e.g. here. In that case the docker command would look more like.

docker run -it -p 3838:3838 -v /path/to/reference:/reference-data:ro azimuth R -e "Azimuth::AzimuthApp(config='/reference-data/config.json')"

[doncarlos999]

This solved the demo dataset problem. Thanks for that.
But now I get another error about missing homolog file:
"Homolog file doesn't exist at path provided:".
I manually downloaded the homolog file from 'https://seurat.nygenome.org/azimuth/references/homologs.rds' and added
homolog.table <- /path/to/homologs.rds; before the Azimuth run command but the error still appears. Is there a way to declare the path to the homolog file?
Thanks again for helping with this.

[andrewwbutler]

You should be able to specify it similarly to the demodataset. E.g.

docker run -it -p 3838:3838 -v /path/to/reference:/reference-data:ro azimuth R -e "Azimuth::AzimuthApp(reference = '/reference-data', demodataset = 'demo.rds', homologs = 'homologs.rds')"

[doncarlos999]

Awesome, looks like it is working perfectly now. Thanks a lot for the help!

[andrewwbutler]

Closing this thread as providing a demodataset should be optional now on the develop branch as of (#64).