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Update dockerfile dependencies
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‎Dockerfile‎

Lines changed: 38 additions & 41 deletions
Original file line numberDiff line numberDiff line change
@@ -457,7 +457,6 @@ RUN \
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apt-get install -y --no-install-recommends gdebi && \
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# Search for files
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apt-get install -y --no-install-recommends catfish && \
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# TODO: Unable to locate package: apt-get install -y --no-install-recommends gnome-search-tool &&
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apt-get install -y --no-install-recommends font-manager && \
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# vs support for thunar
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apt-get install -y thunar-vcs-plugin && \
@@ -591,10 +590,10 @@ RUN \
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conda install -y --update-all \
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'python='$PYTHON_VERSION \
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'ipython=7.19.*' \
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# TODO: notebook > 6.1.x handels terminal creation differently, but a fix is already merged:
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# https://github.com/jupyter/notebook/pull/5813
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'notebook=6.0.3' \
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'notebook=6.1.6' \
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'jupyterlab=2.2.*' \
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# TODO: nbconvert 6.x makes problems with template_path
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'nbconvert=5.6.*' \
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# TODO: temp fix: yarl version 1.5 is required for lots of libraries.
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'yarl==1.5.*' \
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# TODO install scipy, numpy, sklearn, and numexpr via conda for mkl optimizaed versions: https://docs.anaconda.com/mkl-optimizations/
@@ -606,6 +605,8 @@ RUN \
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numexpr && \
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# installed via apt-get and pip: protobuf \
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# installed via apt-get: zlib && \
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# Switch of channel priority, makes some trouble
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conda config --system --set channel_priority false && \
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# Install minimal pip requirements
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pip install --no-cache-dir --upgrade --upgrade-strategy only-if-needed -r ${RESOURCES_PATH}/libraries/requirements-minimal.txt && \
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# If minimal flavor - exit here
@@ -648,14 +649,21 @@ RUN \
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# required for tesseract: 11MB - tesseract-ocr-dev?
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apt-get install -y --no-install-recommends libtesseract-dev && \
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pip install --no-cache-dir tesserocr && \
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# Required for tensorflow graphics (9MB)
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# TODO: installs tenserflow 2.4 - Required for tensorflow graphics (9MB)
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apt-get install -y --no-install-recommends libopenexr-dev && \
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pip install --no-cache-dir tensorflow-graphics==2020.5.20 && \
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#pip install --no-cache-dir tensorflow-graphics==2020.5.20 && \
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# GCC OpenMP (GOMP) support library
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apt-get install -y --no-install-recommends libgomp1 && \
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# Install Intel(R) Compiler Runtime - numba optimization
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# TODO: don't install, results in memory error
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# conda install -y --freeze-installed -c numba icc_rt && \
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# TODO: don't install, results in memory error: conda install -y --freeze-installed -c numba icc_rt && \
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# TODO: problem with channel-prio setting. Install libjpeg turbo for speedup in image processing
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conda install -y --freeze-installed libjpeg-turbo && \
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# TODO: problem with channel-prio setting. Add snakemake for workflow management
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conda install -y -c bioconda -c conda-forge snakemake-minimal && \
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# TODO: problem with channel-prio setting. Add mamba as conda alternativ
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conda install -y -c conda-forge mamba && \
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# TODO: problem with channel-prio setting. Faiss - A library for efficient similarity search and clustering of dense vectors.
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conda install -y --freeze-installed faiss-cpu && \
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# Install full pip requirements
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pip install --no-cache-dir --upgrade --upgrade-strategy only-if-needed -r ${RESOURCES_PATH}/libraries/requirements-full.txt && \
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# Setup Spacy
@@ -732,6 +740,10 @@ RUN \
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clean-layer.sh && \
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exit 0 ; \
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fi && \
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# Install and activate what if tool
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pip install witwidget && \
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jupyter nbextension install --py --symlink --sys-prefix witwidget && \
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jupyter nbextension enable --py --sys-prefix witwidget && \
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# Activate qgrid
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jupyter nbextension enable --py --sys-prefix qgrid && \
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# TODO: Activate Colab support
@@ -771,7 +783,7 @@ RUN \
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pip install jupyterlab-git && \
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jupyter serverextension enable --py jupyterlab_git && \
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# For Matplotlib: https://github.com/matplotlib/jupyter-matplotlib
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$lab_ext_install jupyter-matplotlib && \
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#$lab_ext_install jupyter-matplotlib && \
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# Do not install any other jupyterlab extensions
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if [ "$WORKSPACE_FLAVOR" = "light" ]; then \
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# Final build with minimization
@@ -791,16 +803,17 @@ RUN \
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$lab_ext_install install @jupyter-widgets/jupyterlab-manager plotlywidget && \
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# produces build error: jupyter labextension install jupyterlab-chart-editor && \
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$lab_ext_install jupyterlab-chart-editor && \
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# For holoview
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$lab_ext_install @pyviz/jupyterlab_pyviz && \
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# Install jupyterlab variable inspector - https://github.com/lckr/jupyterlab-variableInspector
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$lab_ext_install @lckr/jupyterlab_variableinspector && \
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# For holoview
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$lab_ext_install @pyviz/jupyterlab_pyviz && \
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# Install Debugger in Jupyter Lab
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# pip install --no-cache-dir xeus-python && \
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# $lab_ext_install @jupyterlab/debugger && \
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# Install jupyterlab code formattor - https://github.com/ryantam626/jupyterlab_code_formatter
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$lab_ext_install @ryantam626/jupyterlab_code_formatter && \
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pip install jupyterlab_code_formatter && \
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# TODO: 1.4.1 forces jupyterlab 3.X
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pip install jupyterlab_code_formatter==1.3.8 && \
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jupyter serverextension enable --py jupyterlab_code_formatter && \
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# Final build with minimization
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jupyter lab build -y --debug-log-path=/dev/stdout --log-level=WARN && \
@@ -852,7 +865,7 @@ RUN \
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cd $RESOURCES_PATH && \
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mkdir -p $HOME/.vscode/extensions/ && \
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# Install python extension - (newer versions are 30MB bigger)
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VS_PYTHON_VERSION="2020.11.371526539" && \
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VS_PYTHON_VERSION="2020.12.424452561" && \
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wget --no-verbose https://github.com/microsoft/vscode-python/releases/download/$VS_PYTHON_VERSION/ms-python-release.vsix && \
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bsdtar -xf ms-python-release.vsix extension && \
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rm ms-python-release.vsix && \
@@ -893,8 +906,7 @@ RUN \
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# && code-server --install-extension formulahendry.code-runner@$VS_CODE_RUNNER_VERSION \
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sleep $SLEEP_TIMER && \
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# Install ESLint extension: https://marketplace.visualstudio.com/items?itemName=dbaeumer.vscode-eslint
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# Older versions do not support vscode 1.39 - https://github.com/microsoft/vscode-eslint/
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VS_ESLINT_VERSION="2.1.13" && \
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VS_ESLINT_VERSION="2.1.14" && \
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wget --retry-on-http-error=429 --waitretry 15 --tries 5 --no-verbose https://marketplace.visualstudio.com/_apis/public/gallery/publishers/dbaeumer/vsextensions/vscode-eslint/$VS_ESLINT_VERSION/vspackage -O dbaeumer.vscode-eslint.vsix && \
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# && wget --no-verbose https://github.com/microsoft/vscode-eslint/releases/download/$VS_ESLINT_VERSION-insider.2/vscode-eslint-$VS_ESLINT_VERSION.vsix -O dbaeumer.vscode-eslint.vsix && \
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bsdtar -xf dbaeumer.vscode-eslint.vsix extension && \
@@ -911,11 +923,13 @@ RUN \
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### INCUBATION ZONE ###
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RUN \
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# Strict channel priority currently makes problems with installing with conda
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conda config --system --set channel_priority false && \
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# apt-get update && \
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# TODO: Fix problem with jupyter extension panel: https://github.com/Jupyter-contrib/jupyter_nbextensions_configurator/issues/125
927+
sed -i 's:notebook/js/mathjaxutils:base/js/mathjaxutils:g' $CONDA_PYTHON_DIR/site-packages/jupyter_nbextensions_configurator/static/nbextensions_configurator/render/render.js && \
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# TODO: Disable pydeck extension, cannot be loaded (404)
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jupyter nbextension disable pydeck/extension && \
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apt-get update && \
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# TODO: lib contains high vulnerability
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# apt-get install -y --no-install-recommends libffi-dev \
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apt-get install -y --no-install-recommends libffi-dev && \
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# Required by magenta
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# apt-get install -y libasound2-dev && \
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# apt-get install -y xfce4-clipman && \
@@ -935,25 +949,8 @@ RUN \
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clean-layer.sh && \
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exit 0 ; \
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fi && \
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# Install libjpeg turbo for speedup in image processing
939-
conda install -y --freeze-installed libjpeg-turbo && \
940-
# Add snakemake for workflow management
941-
conda install -y -c bioconda -c conda-forge snakemake-minimal && \
942-
# Add mamba as conda alternativ
943-
conda install -y -c conda-forge mamba && \
944-
# Faiss - A library for efficient similarity search and clustering of dense vectors.
945-
conda install -y --freeze-installed faiss-cpu && \
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# Install new python libraries
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pip install --no-cache-dir crc32c soundfile GPflow bpytop && \
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# Install fkill-cli
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npm install --global fkill-cli && \
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# Install pretty-errors
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pip install pretty_errors && \
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python -m pretty_errors && \
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# Install what if tool
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pip install witwidget && \
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jupyter nbextension install --py --symlink --sys-prefix witwidget && \
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jupyter nbextension enable --py --sys-prefix witwidget && \
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# Activate pretty-errors
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python -m pretty_errors -u -p && \
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# Cleanup
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clean-layer.sh
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@@ -1115,10 +1112,10 @@ ENV KMP_DUPLICATE_LIB_OK="True" \
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MKL_THREADING_LAYER=GNU \
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# To avoid over-subscription when using TBB, let the TBB schedulers use Inter Process Communication to coordinate:
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ENABLE_IPC=1 \
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# will cause pretty_errors to check if it is running in an interactive terminal
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PYTHON_PRETTY_ERRORS_ISATTY_ONLY=1 \
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# TODO: evaluate - Deactivate hdf5 file locking
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HDF5_USE_FILE_LOCKING=False
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# Activate better python execptions as default
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# TODO: might break stuff BETTER_EXCEPTIONS=1
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HDF5_USE_FILE_LOCKING=False\
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# Set default values for environment variables
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ENV CONFIG_BACKUP_ENABLED="true" \

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