--- a +++ b/torch.Dockerfile @@ -0,0 +1,45 @@ +# syntax=docker/dockerfile:1 +FROM pytorch/pytorch:2.3.1-cuda11.8-cudnn8-runtime +RUN apt update +ARG DEBIAN_FRONTEND=noninteractive +ENV TZ=Etc/UTC + +# Install necessary packages +RUN apt update && \ + apt install -y liblapack-dev libblas-dev libgl1-mesa-glx libsm6 libxext6 wget vim g++ pkg-config libglib2.0-dev expat libexpat-dev libexif-dev libtiff-dev libgsf-1-dev openslide-tools libopenjp2-tools libpng-dev libtiff5-dev libjpeg-turbo8-dev libopenslide-dev python3-tk && \ + sed -i '/^#\sdeb-src /s/^# *//' "/etc/apt/sources.list" && \ + apt update && \ + mkdir /scripts + +# Build libvips 8.15 from source [slideflow requires 8.9+] +RUN apt install build-essential devscripts meson -y && \ + mkdir /libvips && \ + cd /libvips && \ + wget https://github.com/libvips/libvips/archive/refs/tags/v8.15.3.tar.gz && \ + tar zxf v8.15.3.tar.gz && \ + cd /libvips/libvips-8.15.3 && \ + meson setup build --prefix /usr/local/lib && \ + cd /libvips/libvips-8.15.3/build && \ + meson compile && \ + meson install +ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib +ENV SF_VIPS_VERSION=8.15.3 + +# Apply pytorch CuDNN patch +WORKDIR "/opt/conda/lib" +RUN ln -sn libnvrtc.so.11.8.89 libnvrtc.so + +# Install slideflow & download scripts +WORKDIR "/scripts" +ENV SF_BACKEND=torch +RUN pip3 install slideflow[cucim,torch]==3.0.2 cupy-cuda11x slideflow-noncommercial slideflow-gpl versioneer && \ + wget https://raw.githubusercontent.com/slideflow/slideflow/3.0.2/scripts/test.py && \ + wget https://raw.githubusercontent.com/slideflow/slideflow/3.0.2/scripts/slideflow-studio.py && \ + wget https://raw.githubusercontent.com/slideflow/slideflow/3.0.2/scripts/run_project.py && \ + wget https://raw.githubusercontent.com/slideflow/slideflow/3.0.2/scripts/qupath_roi.groovy && \ + wget https://raw.githubusercontent.com/slideflow/slideflow/3.0.2/scripts/qupath_roi_legacy.groovy && \ + wget https://raw.githubusercontent.com/slideflow/slideflow/master/scripts/welcome.py && \ + chmod +x /scripts/welcome.py + +# Set entrypoint +ENTRYPOINT ["bash", "-c", "python3 /scripts/welcome.py && exec /bin/bash"]