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Docker image: Use newer debian stable for the base and newer dcm2niix #790

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Oct 30, 2024
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Docker image: Use newer debian stable for the base and newer dcm2niix #790

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b52a37c
Docker image: Use newer debian stable for the base and newer dcm2niix
yarikoptic Oct 14, 2024
aaabcb0
Make it possible to use podman or docker
yarikoptic Oct 14, 2024
06649a6
updated Dockerfile
yarikoptic Oct 14, 2024
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14 changes: 7 additions & 7 deletions Dockerfile
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Original file line number Diff line number Diff line change
@@ -1,7 +1,7 @@
# Generated by Neurodocker and Reproenv.

FROM neurodebian:bullseye
ENV PATH="/opt/dcm2niix-v1.0.20220720/bin:$PATH"
FROM neurodebian:bookworm
ENV PATH="/opt/dcm2niix-v1.0.20240202/bin:$PATH"
RUN apt-get update -qq \
&& apt-get install -y -q --no-install-recommends \
ca-certificates \
Expand All @@ -16,10 +16,10 @@ RUN apt-get update -qq \
&& git clone https://github.com/rordenlab/dcm2niix /tmp/dcm2niix \
&& cd /tmp/dcm2niix \
&& git fetch --tags \
&& git checkout v1.0.20220720 \
&& 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-v1.0.20220720 .. \
&& 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
Expand Down Expand Up @@ -87,19 +87,19 @@ RUN printf '{ \
{ \
"name": "from_", \
"kwds": { \
"base_image": "neurodebian:bullseye" \
"base_image": "neurodebian:bookworm" \
} \
}, \
{ \
"name": "env", \
"kwds": { \
"PATH": "/opt/dcm2niix-v1.0.20220720/bin:$PATH" \
"PATH": "/opt/dcm2niix-v1.0.20240202/bin:$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 v1.0.20220720\\nmkdir /tmp/dcm2niix/build\\ncd /tmp/dcm2niix/build\\ncmake -DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON -DCMAKE_INSTALL_PREFIX:PATH=/opt/dcm2niix-v1.0.20220720 ..\\nmake -j1\\nmake install\\nrm -rf /tmp/dcm2niix" \
"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" \
} \
}, \
{ \
Expand Down
15 changes: 12 additions & 3 deletions utils/gen-docker-image.sh
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Expand Up @@ -7,11 +7,20 @@ VER=$(grep -Po '(?<=^__version__ = ).*' $thisd/../heudiconv/info.py | sed 's/"//

image="kaczmarj/neurodocker:0.9.1"

docker run --rm $image generate docker \
--base-image neurodebian:bullseye \
if hash podman; then
OCI_BINARY=podman
elif hash docker; then
OCI_BINARY=docker
else
echo "ERROR: no podman or docker found" >&2
exit 1
fi

${OCI_BINARY:-docker} run --rm $image generate docker \
--base-image neurodebian:bookworm \
--pkg-manager apt \
--dcm2niix \
version=v1.0.20220720 \
version=v1.0.20240202 \
method=source \
cmake_opts="-DZLIB_IMPLEMENTATION=Cloudflare -DUSE_JPEGLS=ON -DUSE_OPENJPEG=ON" \
--install \
Expand Down
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