Minimize image

Dockerfile

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-# warning: unofficial base image is not stable and may change in the future!
-FROM docker.io/fnndsc/mni-conda-base:unofficial
+FROM docker.io/fnndsc/pl-fetal-surface-extract:base-1
 
 LABEL org.opencontainers.image.authors="Jennings Zhang <Jennings.Zhang@childrens.harvard.edu>" \
       org.opencontainers.image.title="pl-fetal-surface-extract" \

base/.dockerignore

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+*

base/Dockerfile

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+FROM docker.io/fnndsc/microminc-builder:latest as builder
+
+RUN microminc.sh \
+    adapt_object_mesh \
+    dilate_volume \
+    minccalc \
+    mincchamfer \
+    mincdefrag \
+    mincresample \
+    mincreshape \
+    param2xfm \
+    sphere_mesh \
+    surface_mask2 \
+    transform_objects \
+    inflate_to_sphere_implicit \
+    inflate_to_sphere \
+    create_tetra \
+    print_n_polygons \
+    subdivide_polygons \
+    interpolate_sphere \
+    depth_potential \
+    vertstats_math \
+    volume_object_evaluate \
+    adapt_metric \
+        /microminc
+
+# perl libraries need to be copied manually
+RUN cp -r /opt/CIVET/dist/perl /microminc/perl
+
+# MNI data needs to be copied manually
+RUN mkdir -vp /microminc/share  \
+    && cp -rv "$MNI_DATAPATH/surface-extraction" "/microminc/share"
+
+FROM fnndsc/conda:python3.11.2
+COPY --from=builder /microminc /opt/microminc
+ENV PATH=/opt/microminc/bin:$PATH \
+    LD_LIBRARY_PATH=/opt/microminc/lib:$LD_LIBRARY_PATH \
+    MINC_FORCE_V2=1 MINC_COMPRESS=4 VOLUME_CACHE_THRESHOLD=-1 \
+    MNI_DATAPATH=/opt/microminc/share \
+    PERL5LIB=/opt/microminc/perl

base/README.md

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+Uses [microminc](https://github.com/FNNDSC/microminc)
+to create a minimized base image for `pl-fetal-surface-extract`,
+which copies the necessary minc-tool binaries to a multi-arch conda image.
+
+This image is built and pushed manually.

base/build.sh

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+#!/bin/bash -ex
+
+exec docker buildx build --push \
+    --platform linux/amd64,linux/arm64,linux/ppc64le \
+    --build-arg http_proxy=$http_proxy \
+    -t docker.io/fnndsc/pl-fetal-surface-extract:base-1 .