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BodenmillerGroup / steinbock

A toolkit for processing multiplexed tissue images
https://bodenmillergroup.github.io/steinbock
MIT License
49 stars 14 forks source link

Document & test use with singularity #159

Open jwindhager opened 1 year ago

jwindhager commented 1 year ago

See #155

jwindhager commented 1 year ago

Something like this should work starting from steinbock 0.16.0 (untested):

singularity run --bind /mnt/data/git/steinbock/data:/data --env RUN_FIXUID= docker://ghcr.io/bodenmillergroup/steinbock:0.16.0

This may also make running GUI applications such as napari much easier.

Elena983 commented 7 months ago

Hi Jonas

I download the steinbock, but can’t run the commands image

jwindhager commented 7 months ago

Hoi @Elena983,

I haven't tested using steinbock with Singularity myself, and steinbock is now in the hands of @Milad4849, but from your screenshot it appears that you'd need to adapt your steinbock command alias to use singularity instead of docker. You can check here how to use the singularity run command, and compare it with docker run.

Elena983 commented 7 months ago

Thank you I discovered that docker run -v equals to singularity run --bind But it still gives an error image

jwindhager commented 7 months ago

Please compare your alias with https://github.com/BodenmillerGroup/steinbock/issues/159#issuecomment-1416490900, e.g. regarding the use of --env RUN_FIXUID= and docker://

Elena983 commented 7 months ago

Yes, I run it. Many thanks

Elena983 commented 7 months ago

but now it didn't see the folders in it, but I double checked the path image