heudiconv (latest)
Installation
docker pull hub.trr379.de/q02/heudiconv:latestsha256:7d6a8ea0cce7c7c7f04f71fc1fbe2e3f8dc887136c33fe55d60574f76caa01bcImage layers
| # debian.sh --arch 'amd64' out/ 'bookworm' '@1742169600' |
| RUN /bin/sh -c set -x && apt-get update && { which gpg || apt-get install -y --no-install-recommends gnupg ; } && { gpg --version | grep -q '^gpg (GnuPG) 1\.' || apt-get install -y --no-install-recommends dirmngr ; } && rm -rf /var/lib/apt/lists/* # buildkit |
| RUN /bin/sh -c set -x && export GNUPGHOME="$(mktemp -d)" && gpg --batch --keyserver keyserver.ubuntu.com --recv-keys DD95CC430502E37EF840ACEEA5D32F012649A5A9 && mkdir -p /etc/apt/keyrings && gpg --batch --export --armor DD95CC430502E37EF840ACEEA5D32F012649A5A9 > /etc/apt/keyrings/neurodebian.asc && rm -rf "$GNUPGHOME" # buildkit |
| RUN /bin/sh -c { echo 'deb [signed-by=/etc/apt/keyrings/neurodebian.asc] http://neuro.debian.net/debian bookworm main'; echo 'deb [signed-by=/etc/apt/keyrings/neurodebian.asc] http://neuro.debian.net/debian data main'; echo '#deb-src [signed-by=/etc/apt/keyrings/neurodebian.asc] http://neuro.debian.net/debian-devel bookworm main'; } > /etc/apt/sources.list.d/neurodebian.sources.list # buildkit |
| RUN /bin/sh -c set -x && apt-get update && apt-get install -y --no-install-recommends neurodebian-freeze eatmydata && ln -s /usr/bin/eatmydata /usr/local/bin/apt-get && rm -rf /var/lib/apt/lists/* # buildkit |
| ENV PATH=/opt/dcm2niix-v1.0.20240202/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin |
| RUN /bin/sh -c apt-get update -qq && apt-get install -y -q --no-install-recommends ca-certificates cmake g++ gcc git make pigz zlib1g-dev && rm -rf /var/lib/apt/lists/* && git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix && cd /tmp/dcm2niix && git fetch --tags && git checkout v1.0.20240202 && mkdir /tmp/dcm2niix/build && cd /tmp/dcm2niix/build && cmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20240202 .. && make -j1 && make install && rm -rf /tmp/dcm2niix # buildkit |
| RUN /bin/sh -c apt-get update -qq && apt-get install -y -q --no-install-recommends gcc git git-annex-standalone libc-dev liblzma-dev netbase pigz && rm -rf /var/lib/apt/lists/* # buildkit |
| COPY . /src/heudiconv # buildkit |
| ENV CONDA_DIR=/opt/miniconda-py39_4.12.0 PATH=/opt/miniconda-py39_4.12.0/bin:/opt/dcm2niix-v1.0.20240202/bin:/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin |
| RUN /bin/sh -c apt-get update -qq && apt-get install -y -q --no-install-recommends bzip2 ca-certificates curl && rm -rf /var/lib/apt/lists/* && export PATH="/opt/miniconda-py39_4.12.0/bin:$PATH" && echo "Downloading Miniconda installer ..." && conda_installer="/tmp/miniconda.sh" && curl -fsSL -o "$conda_installer" https://repo.continuum.io/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh && bash "$conda_installer" -b -p /opt/miniconda-py39_4.12.0 && rm -f "$conda_installer" && conda config --system --prepend channels conda-forge && conda config --set channel_priority strict && conda config --system --set auto_update_conda false && conda config --system --set show_channel_urls true && conda init bash && conda install -y --name base "python=3.9" "traits>=4.6.0" "scipy" "numpy" "nomkl" "pandas" "gdcm" && bash -c "source activate base && python -m pip install --no-cache-dir --editable "/src/heudiconv[all]"" && sync && conda clean --all --yes && sync && rm -rf ~/.cache/pip/* # buildkit |
| ENTRYPOINT ["heudiconv"] |
| RUN /bin/sh -c printf '{ "pkg_manager": "apt", "existing_users": [ "root" ], "instructions": [ { "name": "from_", "kwds": { "base_image": "neurodebian:bookworm" } }, { "name": "env", "kwds": { "PATH": "/opt/dcm2niix-v1.0.20240202/bin:$PATH" } }, { "name": "run", "kwds": { "command": "apt-get update -qq\\napt-get install -y -q --no-install-recommends \\\\\\n ca-certificates \\\\\\n cmake \\\\\\n g++ \\\\\\n gcc \\\\\\n git \\\\\\n make \\\\\\n pigz \\\\\\n zlib1g-dev\\nrm -rf /var/lib/apt/lists/*\\ngit clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix\\ncd /tmp/dcm2niix\\ngit fetch --tags\\ngit checkout v1.0.20240202\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20240202 ..\\nmake -j1\\nmake install\\nrm -rf /tmp/dcm2niix" } }, { "name": "install", "kwds": { "pkgs": [ "git", "gcc", "pigz", "liblzma-dev", "libc-dev", "git-annex-standalone", "netbase" ], "opts": null } }, { "name": "run", "kwds": { "command": "apt-get update -qq \\\\\\n && apt-get install -y -q --no-install-recommends \\\\\\n gcc \\\\\\n git \\\\\\n git-annex-standalone \\\\\\n libc-dev \\\\\\n liblzma-dev \\\\\\n netbase \\\\\\n pigz \\\\\\n && rm -rf /var/lib/apt/lists/*" } }, { "name": "copy", "kwds": { "source": [ ".", "/src/heudiconv" ], "destination": "/src/heudiconv" } }, { "name": "env", "kwds": { "CONDA_DIR": "/opt/miniconda-py39_4.12.0", "PATH": "/opt/miniconda-py39_4.12.0/bin:$PATH" } }, { "name": "run", "kwds": { "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-py39_4.12.0/bin:$PATH\\"\\necho \\"Downloading Miniconda installer ...\\"\\nconda_installer=\\"/tmp/miniconda.sh\\"\\ncurl -fsSL -o \\"$conda_installer\\" https://repo.continuum.io/miniconda/Miniconda3-py39_4.12.0-Linux-x86_64.sh\\nbash \\"$conda_installer\\" -b -p /opt/miniconda-py39_4.12.0\\nrm -f \\"$conda_installer\\"\\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\\" \\\\\\n \\"gdcm\\"\\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/*" } }, { "name": "entrypoint", "kwds": { "args": [ "heudiconv" ] } } ] }' > /.reproenv.json # buildkit |
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