Document & test use with singularity

[jwindhager]

See #155

[jwindhager]

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]

Hi Jonas

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

[jwindhager]

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]

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

[jwindhager]

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]

Yes, I run it. Many thanks

[Elena983]

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