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Docker Container

A docker container for pybioclip is hosted at ghcr.io. This container has CPU support for Mac, Windows, and Linux. GPU(CUDA) support is only for Windows and Linux. In order to access your images the docker container requires you to mount a volume. To avoid redownloading various bioclip files mounting a volume to hold a .cache directory is recommended. By default the working and home directories for this container are both set to /home/bcuser.

All examples below require an image file named Ursus-arctos.jpeg in the current directory.

Mac/Linux CPU Usage

docker run --platform linux/amd64 -v $(pwd):/home/bcuser -it ghcr.io/imageomics/pybioclip:1.0.0 bioclip predict Ursus-arctos.jpeg

Linux GPU Usage

docker run --gpus all --platform linux/amd64 -v $(pwd):/home/bcuser -it ghcr.io/imageomics/pybioclip:1.0.0 bioclip predict --device cuda Ursus-arctos.jpeg

Windows CPU Usage

docker run -it -v %cd%:/home/bcuser ghcr.io/imageomics/pybioclip:1.0.0 bioclip predict Ursus-arctos.jpeg

Windows GPU Usage

docker run -it --gpus all -v %cd%:/home/bcuser ghcr.io/imageomics/pybioclip bioclip:1.0.0 predict --device cuda Ursus-arctos.jpeg