Containers do not appear to include Wine64, zugbruecke for PL2 files

[nikhilchandra]

I might not fully understand how everything works, but would a Docker container (and presumably a Singularity container) for one of the spike sorters (say, spikeinterface/kilosort4-base) need to include Wine64 and zugbruecke in order to work with PL2 files? Out of curiosity I tried running the run_sorter method for kilosort4 with docker_image=True and got an error message that indicated the absence of Wine. Thanks!

@cheydrick

[zm711]

yes it would. the docker containers (singularity I don't know) are going to be linux-esque. So if you wanted to use docker for plexon2 stuff you would need to include wine in the extras. @alejoe91 knows way more about the docker stuff than me so he could give you specifics for commands.

[alejoe91]

Right @zm711

It would be very tricky to install it on the fly, so I suggest that if you have a .pl2 file and want to run it in a container, the best way would be to convert it to binary.

[nikhilchandra]

@alejoe91 Is it unfeasible to include wine64 and pickle in the Docker container from the get-go? This would the negate the need for installing on the fly and also avoid conversion to BIN.

[alejoe91]

The containers tend to have minimal installations of the sorters dependencies only, so that they are easier to maintain and upgrade.

What you could do is build a docker image FROM a spikeinterface container and add the additional wine dependencies and distribute tham as something like: spikeinterface-pl2/kilosort4-base, etc.

When running a sorter, then you can specify the exact image to use as a container!

[nikhilchandra]

I see, that makes sense. Thank you!

@cheydrick