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# Generated by Neurodocker and Reproenv.
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FROM neurodebian:bullseye
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- ENV PATH="/opt/dcm2niix-v1.0.20211006 /bin:$PATH"
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+ ENV PATH="/opt/dcm2niix-v1.0.20220720 /bin:$PATH"
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RUN apt-get update -qq \
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&& apt-get install -y -q --no-install-recommends \
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ca-certificates \
@@ -16,10 +16,10 @@ RUN apt-get update -qq \
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&& git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
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&& cd /tmp/dcm2niix \
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&& git fetch --tags \
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- && git checkout v1.0.20211006 \
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+ && git checkout v1.0.20220720 \
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&& mkdir /tmp/dcm2niix/build \
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&& cd /tmp/dcm2niix/build \
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- && cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20211006 .. \
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+ && cmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 .. \
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&& make -j1 \
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&& make install \
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&& rm -rf /tmp/dcm2niix
@@ -63,7 +63,7 @@ RUN apt-get update -qq \
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# Enable `conda activate`
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&& conda init bash \
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&& conda install -y --name base \
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- "python=3.7 " \
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+ "python=3.9 " \
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"traits>=4.6.0" \
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"scipy" \
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"numpy" \
@@ -93,13 +93,13 @@ RUN printf '{ \
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{ \
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"name": "env", \
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"kwds": { \
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- "PATH": "/opt/dcm2niix-v1.0.20211006 /bin:$PATH" \
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+ "PATH": "/opt/dcm2niix-v1.0.20220720 /bin:$PATH" \
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} \
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}, \
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{ \
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"name": "run", \
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"kwds": { \
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- "command": "apt-get update -qq\\ napt-get install -y -q --no-install-recommends \\\\\\ n ca-certificates \\\\\\ n cmake \\\\\\ n g++ \\\\\\ n gcc \\\\\\ n git \\\\\\ n make \\\\\\ n pigz \\\\\\ n zlib1g-dev\\ nrm -rf /var/lib/apt/lists/*\\ ngit clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix\\ ncd /tmp/dcm2niix\\ ngit fetch --tags\\ ngit checkout v1.0.20211006 \\ nmkdir /tmp/dcm2niix/build\\ ncd /tmp/dcm2niix/build\\ ncmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20211006 ..\\ nmake -j1\\ nmake install\\ nrm -rf /tmp/dcm2niix" \
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+ "command": "apt-get update -qq\\ napt-get install -y -q --no-install-recommends \\\\\\ n ca-certificates \\\\\\ n cmake \\\\\\ n g++ \\\\\\ n gcc \\\\\\ n git \\\\\\ n make \\\\\\ n pigz \\\\\\ n zlib1g-dev\\ nrm -rf /var/lib/apt/lists/*\\ ngit clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix\\ ncd /tmp/dcm2niix\\ ngit fetch --tags\\ ngit checkout v1.0.20220720 \\ nmkdir /tmp/dcm2niix/build\\ ncd /tmp/dcm2niix/build\\ ncmake -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 ..\\ nmake -j1\\ nmake install\\ nrm -rf /tmp/dcm2niix" \
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} \
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}, \
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{ \
@@ -143,7 +143,7 @@ RUN printf '{ \
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{ \
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"name": "run", \
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"kwds": { \
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- "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-latest/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-latest\\nrm -f \\"$conda_installer\\"\\nconda update -yq -nbase conda\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y --name base \\\\\\n \\"python=3.7\\" \\\\\\n \\"traits>=4.6.0\\" \\\\\\n \\"scipy\\" \\\\\\n \\"numpy\\" \\\\\\n \\"nomkl\\" \\\\\\n \\"pandas\\"\\nbash -c \\"source activate base\\n python -m pip install --no-cache-dir --editable \\\\\\n \\"/src/heudiconv[all]\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
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+ "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n bzip2 \\\\\\n ca-certificates \\\\\\n curl\\nrm -rf /var/lib/apt/lists/*\\n# Install dependencies.\\nexport PATH=\\"/opt/miniconda-latest/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-latest-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-latest\\nrm -f \\"$conda_installer\\"\\nconda update -yq -nbase conda\\n# Prefer packages in conda-forge\\nconda config --system --prepend channels conda-forge\\n# Packages in lower-priority channels not considered if a package with the same\\n# name exists in a higher priority channel. Can dramatically speed up installations.\\n# Conda recommends this as a default\\n# https://docs.conda.io/projects/conda/en/latest/user-guide/tasks/manage-channels.html\\nconda config --set channel_priority strict\\nconda config --system --set auto_update_conda false\\nconda config --system --set show_channel_urls true\\n# Enable `conda activate`\\nconda init bash\\nconda install -y --name base \\\\\\n \\"python=3.9\\" \\\\\\n \\"traits>=4.6.0\\" \\\\\\n \\"scipy\\" \\\\\\n \\"numpy\\" \\\\\\n \\"nomkl\\" \\\\\\n \\"pandas\\"\\nbash -c \\"source activate base\\n python -m pip install --no-cache-dir --editable \\\\\\n \\"/src/heudiconv[all]\\"\\"\\n# Clean up\\nsync && conda clean --all --yes && sync\\nrm -rf ~/.cache/pip/*" \
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} \
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}, \
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{ \
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