Docker container for tabular data predictions

A GPU-enabled environment for tabular predictions with TabICL, including its fine-tuning and SHAP extras.

Container environment

The Dockerfile uses pytorch/pytorch:2.13.0-cuda13.0-cudnn9-runtime as its runtime base. It specifies Python 3.12, PyTorch 2.13.0 with CUDA 13.0, and cuDNN 9. This is a runtime image; it does not include the CUDA development toolkit.

The following packages are installed into the base Python environment:

Package	Version	Extras
tabicl	2.1.1	finetune, shap
matplotlib	3.11.1
pandas	2.3.3

uv and uvx are copied from ghcr.io/astral-sh/uv:latest. Package installation uses uv pip install --system --break-system-packages to reuse the base image's CUDA-enabled PyTorch environment.

The working directory is /work. Python bytecode generation is disabled, Python output is unbuffered, and uv uses no cache and copies files when linking. HF_HOME is commented out in the Dockerfile, so the image does not explicitly set a Hugging Face cache location.

Build

From the directory containing the Dockerfile:

docker build -t docker-tabular:latest .

Run

GPU access requires a host with a compatible NVIDIA driver and Docker GPU support configured through the NVIDIA Container Toolkit.

Start an interactive shell:

docker run -it --rm --gpus all docker-tabular:latest bash

Mount the current directory at /work to access local scripts and data and retain output files on the host:

docker run -it --rm --gpus all \
  -v "$PWD:/work" \
  docker-tabular:latest bash

To run a local script directly, replace predict.py with your script name:

docker run --rm --gpus all \
  -v "$PWD:/work" \
  docker-tabular:latest python predict.py

The Dockerfile does not copy application code or data into the image or define a custom entrypoint or command.

Use with a Galaxy tool

With Planemo installed on the host and a tabular-prediction.xml tool definition that references the appropriate container image, run:

planemo serve --docker_run_extra_arguments "--gpus all" --docker tabular-prediction.xml

Planemo and the tool XML are not included in this repository or installed by this Dockerfile.