/opt/docker/entrypoint.sh

/opt/toolkit

MONAI_INSTALL_GITHASH= MONAILABEL_INSTALL_GITHASH= REQUIREMENTS_FILE=docker/monai-toolkit/requirements-release.txt chmod 777 -R /opt/docker &&
  mkdir -p ${MONAI_DATA_DIRECTORY} &&
  jupyter labextension disable "@jupyterlab/apputils-extension:announcements" &&
  sed -i 's/NotebookApp/ServerApp/g' /usr/local/etc/jupyter/jupyter_notebook_config.py &&
  sed -i "s|c.ServerApp.root_dir = '/workspace'|c.ServerApp.root_dir = '/opt/toolkit'|g" /usr/local/etc/jupyter/jupyter_notebook_config.py &&
  for i in "tooltracking" "inbody" "deepedit"; do sed -i 's/projectmonai\/monailabel:latest/nvcr.io\/nvidia\/clara\/monai-toolkit/' /usr/local/monailabel/plugins/cvat/endoscopy/${i}.yaml; sed -i '/preCopy/a \        - kind: ENTRYPOINT\n\          value: ' /usr/local/monailabel/plugins/cvat/endoscopy/${i}.yaml; done &&
  echo PATH=$PATH > /etc/environment

MONAI_INSTALL_GITHASH= MONAILABEL_INSTALL_GITHASH= REQUIREMENTS_FILE=docker/monai-toolkit/requirements-release.txt pip uninstall -y grpcio &&
  pip install --disable-pip-version-check --no-cache-dir nvflare==${NVFLARE_VER} monai-nvflare==${MONAI_NVFLARE_VER} &&
  pip uninstall -y grpcio &&
  pip install --no-cache-dir --disable-pip-version-check --no-deps grpcio==1.62.1 # fix grpcio version

MONAI_INSTALL_GITHASH= MONAILABEL_INSTALL_GITHASH= REQUIREMENTS_FILE=docker/monai-toolkit/requirements-release.txt if [ -z "$MONAILABEL_INSTALL_GITHASH" ]; then pip install --disable-pip-version-check --no-deps monailabel==${MONAI_LABEL_VER}; else pip install --disable-pip-version-check --no-deps git+https://github.com/Project-MONAI/MONAILabel@${MONAILABEL_INSTALL_GITHASH}#egg=monailabel; fi

MONAI_INSTALL_GITHASH= MONAILABEL_INSTALL_GITHASH= REQUIREMENTS_FILE=docker/monai-toolkit/requirements-release.txt if [ -z "$MONAI_INSTALL_GITHASH" ]; then pip install --disable-pip-version-check --no-cache-dir monai==${MONAI_VER}; else BUILD_MONAI=$( [ "$ARCH" = "arm64" ] &&
  echo 0 ||
  echo 1 ) &&
  pip install --disable-pip-version-check --no-cache-dir git+https://github.com/Project-MONAI/MONAI@${MONAI_INSTALL_GITHASH}#egg=monai; fi

MONAI_INSTALL_GITHASH= MONAILABEL_INSTALL_GITHASH= REQUIREMENTS_FILE=docker/monai-toolkit/requirements-release.txt jupyter lab clean &&
  pip install --no-cache-dir --disable-pip-version-check -r /tmp/requirements.txt &&
  pip install --no-cache-dir --disable-pip-version-check --no-deps pydicom-seg

MONAI_INSTALL_GITHASH= MONAILABEL_INSTALL_GITHASH= REQUIREMENTS_FILE=docker/monai-toolkit/requirements-release.txt set -ex &&
  ARCH=$(uname -m) &&
  if [ "$ARCH" = "aarch64" ]; then export CFLAGS="-O3" &&
  export DISABLE_NUMCODECS_SSE2=true &&
  export DISABLE_NUMCODECS_AVX2=true &&
  pip install --disable-pip-version-check --no-cache-dir numcodecs==0.11.0; ARCH="arm64"; else ARCH="amd64"; fi &&
  apt-get update -y &&
  DEBIAN_FRONTEND="noninteractive" apt-get install -y --no-install-recommends libopenslide0 &&
  wget "https://launchpad.net/ubuntu/+archive/primary/+files/libsharpyuv0_1.3.2-0.4build3_${ARCH}.deb" &&
  wget "https://launchpad.net/ubuntu/+archive/primary/+files/libwebp7_1.3.2-0.4build3_${ARCH}.deb" &&
  dpkg -i "libsharpyuv0_1.3.2-0.4build3_${ARCH}.deb" &&
  dpkg -i "libwebp7_1.3.2-0.4build3_${ARCH}.deb" &&
  rm -f "libsharpyuv0_1.3.2-0.4build3_${ARCH}.deb" "libwebp7_1.3.2-0.4build3_${ARCH}.deb"

monai-toolkit-workspace.json /root/.jupyter/lab/workspaces/default-37a8.jupyterlab-workspace

monai_styling /usr/local/share/jupyter/labextensions/monai_styling