63 lines
2.1 KiB
Docker
Executable file
63 lines
2.1 KiB
Docker
Executable file
# FROM nvcr.io/nvidia/clara-train-sdk:v4.1
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FROM nvcr.io/nvidia/pytorch:22.08-py3
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# apt
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RUN apt-get update -y \
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&& apt-get install libxrender1 openssh-server pigz sudo -y
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#conda
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# RUN conda update -y -n base conda
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# RUN conda install -y -n base conda-libmamba-solver
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# RUN conda config -y --set solver libmamba
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# pip
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# RUN pip install --upgrade pip
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# RUN pip install antspyx itk-elastix nipype nnunet rt_utils
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RUN pip install antspyx nipype nnunet nnunetv2 simpleitk==2.3.1 tensorflow # too large .... install first
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# RUN pip install itk-elastix==0.13.0
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# RUN pip install itk-elastix
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# RUN pip install --upgrade git+https://github.com/FabianIsensee/hiddenlayer.git@more_plotted_details#egg=hiddenlayer
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# RUN pip install --upgrade git+https://github.com/FabianIsensee/hiddenlayer.git
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# RUN pip install --upgrade git+https://github.com/rohitrango/fireants.git
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# RUN pip install git+https://github.com/qurit/rt-utils.git@5bab9ffcc8fe19dd775e940afdc3d8f48f869150 # fix FrameOfReferenceUID
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# RUN pip install git+https://github.com/adalca/neurite.git git+https://github.com/freesurfer/surfa.git git+https://github.com/voxelmorph/voxelmorph.git
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# WORKDIR /workspace
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WORKDIR /123
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COPY requirements.txt /123
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RUN pip install -r requirements.txt
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RUN wget https://github.com/rordenlab/dcm2niix/releases/download/v1.0.20240202/dcm2niix_lnx.zip
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RUN unzip dcm2niix_lnx.zip
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RUN cp dcm2niix /usr/bin
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# nnUNet
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ENV nnUNet_raw_data_base="/workspace/nnUNet_raw_data_base"
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ENV nnUNet_preprocessed="/workspace/nnUNet_preprocessed"
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ENV RESULTS_FOLDER="/workspace/nnUNet_trained_models"
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ENV nnUNet_raw="/workspace/v2/nnUNet_raw"
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ENV nnUNet_preprocessed="/workspace/v2/nnUNet_preprocessed"
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ENV nnUNet_results="/workspace/v2/nnUNet_results"
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# SSH server
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#RUN echo 'root:password' | chpasswd
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#RUN echo "PasswordAuthentication yes" >> /etc/ssh/sshd_config
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#RUN echo "PermitRootLogin yes" >> /etc/ssh/sshd_config
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#ENTRYPOINT service ssh restart && env >> /etc/environment && bash
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#EXPOSE 22
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# Masonite
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EXPOSE 8000
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# jupyter
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ENTRYPOINT jupyter-lab
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EXPOSE 8888
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# pynetdicom
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EXPOSE 11120
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