123/docker/v1/Dockerfile

FROM nvcr.io/nvidia/clara-train-sdk:v4.1

# apt
RUN apt-get update -y \
&&  apt-get install openssh-server pigz sudo  -y

# pip
# RUN pip install antspyx itk-elastix nipype nnunet rt_utils
RUN pip install antspyx nipype nnunet          # too large .... install first
RUN pip install itk-elastix==0.13.0
RUN pip install --upgrade git+https://github.com/FabianIsensee/hiddenlayer.git@more_plotted_details#egg=hiddenlayer
RUN pip install git+https://github.com/qurit/rt-utils.git@5bab9ffcc8fe19dd775e940afdc3d8f48f869150          # fix FrameOfReferenceUID


# WORKDIR /workspace
WORKDIR /123
COPY requirements.txt /123
RUN pip install -r requirements.txt

RUN wget https://github.com/rordenlab/dcm2niix/releases/download/v1.0.20240202/dcm2niix_lnx.zip
RUN unzip dcm2niix_lnx.zip
RUN cp dcm2niix /usr/bin

# nnUNet

ENV nnUNet_raw_data_base="/workspace/nnUNet_raw_data_base"
ENV nnUNet_preprocessed="/workspace/nnUNet_preprocessed"
ENV RESULTS_FOLDER="/workspace/nnUNet_trained_models"

# SSH server
#RUN echo 'root:password' | chpasswd
#RUN echo "PasswordAuthentication yes" >> /etc/ssh/sshd_config
#RUN echo "PermitRootLogin yes" >> /etc/ssh/sshd_config
#ENTRYPOINT service ssh restart && env >> /etc/environment && bash
#EXPOSE 22

# Masonite
EXPOSE 8000

# jupyter
ENTRYPOINT jupyter-lab
EXPOSE 8888

# pynetdicom
EXPOSE 11120