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Models:
Daniel Galbraith
DanielG/
PathFlowAI
0
Downloads: 1
[27c943]: / docker / Singularity

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Bootstrap: docker

From: nvidia/cuda:10.1-devel-ubuntu18.04



%post

   apt-get update -y

   apt install -y build-essential

   DEBIAN_FRONTEND=noninteractive apt-get install -y --no-install-recommends \

         wget \

         python3 \

         python3-tk \

         python3-pip \

         cmake \

         git \

         openslide-tools \

         libsm6 \

         libxext6 \

         libxrender-dev



   rm -rf /var/lib/apt/lists/*



   wget https://repo.anaconda.com/archive/Anaconda3-2020.02-Linux-x86_64.sh -O ~/anaconda3.sh

   bash ~/anaconda3.sh -b -p /home/anaconda3

   rm ~/anaconda3.sh

   echo "export PATH=/home/anaconda3/bin:$PATH" >> ~/.bashrc

   /bin/bash -c "source /root/.bashrc"



   echo "source /home/anaconda3/etc/profile.d/conda.sh" >> /.singularity_bash



   export PATH=/home/anaconda3/bin:$PATH



   wget https://raw.githubusercontent.com/jlevy44/PathFlowAI/master/docker/spec-list.pathflow.txt



   conda create --name default --file spec-list.pathflow.txt && \

      rm spec-list.pathflow.txt



   conda install -y numpy ninja pyyaml mkl mkl-include setuptools cmake cffi



   export TORCH_CUDA_ARCH_LIST="5.0 5.2 5.3 6.0 6.2 7.0 7.2 7.5"



   export TORCH=4



   export CUDA=cu101



   pip install torch==1.4.0 torchvision==0.5.0 -f https://download.pytorch.org/whl/cu101/torch-1.4.0-cp37-cp37m-linux_x86_64.whl --upgrade



   mkdir -p $SINGULARITY_ROOTFS/tmp/sing_build_cuda

   cd $SINGULARITY_ROOTFS/tmp/sing_build_cuda



   wget https://raw.githubusercontent.com/jlevy44/PathFlowAI/master/docker/requirements.txt



   pip install -r requirements.txt && \

       rm requirements.txt



   pip install git+https://github.com/jlevy44/PathFlowAI.git



   install_apex



   pip install opencv-python-headless histomicstk girder-large-image girder-slicer-cli-web --find-links https://girder.github.io/large_image_wheels



   cd $CURDIR

   rm -rf $SINGULARITY_ROOTFS/tmp/sing_build_cuda







%runScript

   LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/cuda/lib64

   export PATH="/home/anaconda3/bin:/usr/local/bin:/usr/bin:/bin:"

   unset CONDA_DEFAULT_ENV

   export ANACONDA_HOME=/home/anaconda3





%environment

      CPATH="/usr/local/cuda/include:$CPATH"

      PATH="/usr/local/cuda/bin:$PATH"

      LD_LIBRARY_PATH="/usr/local/cuda/lib64:$LD_LIBRARY_PATH"

      CUDA_HOME="/usr/local/cuda"

      CONDA_INSTALL_PATH="/home/anaconda3"

      CONDA_BIN_PATH="/home/anaconda3/bin"

      export PATH="$CONDA_BIN_PATH:$PATH"

      export CPATH PATH LD_LIBRARY_PATH CUDA_HOME