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WIP: strip dockerfile #128

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WIP: strip dockerfile #128

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12 changes: 7 additions & 5 deletions Dockerfile
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Original file line number Diff line number Diff line change
Expand Up @@ -51,10 +51,12 @@
apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*

# FreeSurfer 7.4.1
# FROM downloader AS freesurfer
# COPY docker/files/freesurfer7.4.1-exclude.txt /usr/local/etc/freesurfer7.4.1-exclude.txt
# RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz \
# | tar zxv --no-same-owner -C /opt --exclude-from=/usr/local/etc/freesurfer7.4.1-exclude.txt
FROM downloader AS freesurfer
COPY docker/files/freesurfer7.4.1-exclude.txt /tmp/freesurfer7.4.1-exclude.txt
RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/7.4.1/freesurfer-linux-ubuntu22_amd64-7.4.1.tar.gz -o /tmp/freesurfer.tar.gz \
&& tar -xzf /tmp/freesurfer.tar.gz --no-same-owner -C /opt --exclude-from=/tmp/freesurfer7.4.1-exclude.txt \
&& rm -rf /tmp/freesurfer.tar.gz /tmp/freesurfer7.4.1-exclude.txt \
&& rm -rf /opt/freesurfer/{docs,subjects/bert,subjects/cvs_avg35,subjects/cvs_avg35_inMNI152,subjects/fsaverage3,subjects/fsaverage4,subjects/fsaverage_sym,subjects/lh.EC_average,subjects/rh.EC_average,subjects/sample-001.mgz,subjects/sample-002.mgz,subjects/V1_average,trctrain,matlab,mni-1.4,mni/bin,mni/include,mni/share,lib/qt,lib/vtk}

# AFNI
FROM downloader AS afni
Expand Down Expand Up @@ -173,7 +175,7 @@
&& ldconfig

# Install files from stages
COPY --from=freesurfer/freesurfer:7.4.1 /usr/local/freesurfer /opt/freesurfer
COPY --from=freesurfer /opt/freesurfer /opt/freesurfer
COPY --from=afni /opt/afni-latest /opt/afni-latest
COPY --from=petpvc /usr/local /usr/local

Expand Down Expand Up @@ -202,7 +204,7 @@
# Create a shared $HOME directory
RUN useradd -m -s /bin/bash -G users petprep
WORKDIR /home/petprep
ENV HOME="/home/petprep" \

Check warning on line 207 in Dockerfile

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GitHub Actions / build-container

Variables should be defined before their use 

UndefinedVar: Usage of undefined variable '$LD_LIBRARY_PATH'
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/
LD_LIBRARY_PATH="/usr/lib/x86_64-linux-gnu:${LD_LIBRARY_PATH:-}"

COPY --from=micromamba /bin/micromamba /bin/micromamba
Expand All @@ -211,7 +213,7 @@
ENV MAMBA_ROOT_PREFIX="/opt/conda"
RUN micromamba shell init -s bash && \
echo "micromamba activate petprep" >> $HOME/.bashrc
ENV PATH="/opt/conda/envs/petprep/bin:$PATH" \

Check warning on line 216 in Dockerfile

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GitHub Actions / build-container

Variables should be defined before their use 

UndefinedVar: Usage of undefined variable '$CPATH' (did you mean $PATH?)
More info: https://docs.docker.com/go/dockerfile/rule/undefined-var/
CPATH="/opt/conda/envs/petprep/include:${CPATH:-}" \
LD_LIBRARY_PATH="/opt/conda/envs/petprep/lib:$LD_LIBRARY_PATH"

Expand Down