From 29a4c610c3ad613ce221c9c083751e3da86073b6 Mon Sep 17 00:00:00 2001
From: Jennings Zhang <Jennings.Zhang@childrens.harvard.edu>
Date: Fri, 28 Apr 2023 13:45:08 -0400
Subject: [PATCH] Minimize image

---
 Dockerfile         |  3 +--
 base/.dockerignore |  1 +
 base/Dockerfile    | 40 ++++++++++++++++++++++++++++++++++++++++
 base/README.md     |  5 +++++
 base/build.sh      |  6 ++++++
 5 files changed, 53 insertions(+), 2 deletions(-)
 create mode 100644 base/.dockerignore
 create mode 100644 base/Dockerfile
 create mode 100644 base/README.md
 create mode 100755 base/build.sh

diff --git a/Dockerfile b/Dockerfile
index 902d725..fa54d73 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,5 +1,4 @@
-# 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" \
diff --git a/base/.dockerignore b/base/.dockerignore
new file mode 100644
index 0000000..f59ec20
--- /dev/null
+++ b/base/.dockerignore
@@ -0,0 +1 @@
+*
\ No newline at end of file
diff --git a/base/Dockerfile b/base/Dockerfile
new file mode 100644
index 0000000..7a5533a
--- /dev/null
+++ b/base/Dockerfile
@@ -0,0 +1,40 @@
+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:$LD_LIBRARY_PATH \
+    MINC_FORCE_V2=1 MINC_COMPRESS=4 VOLUME_CACHE_THRESHOLD=-1 \
+    MNI_DATAPATH=/opt/microminc/share \
+    PERL5LIB=/opt/microminc/perl
diff --git a/base/README.md b/base/README.md
new file mode 100644
index 0000000..8cb5e7f
--- /dev/null
+++ b/base/README.md
@@ -0,0 +1,5 @@
+Uses [microminc](https://github.com/FNNDSC/microminc)
+to create a minimized base image for `pl-fetal-surface-extract`,
+which copies the necessary minc-tool binaries to a multi-arch conda image.
+
+This image is built and pushed manually.
diff --git a/base/build.sh b/base/build.sh
new file mode 100755
index 0000000..c7dfa5e
--- /dev/null
+++ b/base/build.sh
@@ -0,0 +1,6 @@
+#!/bin/bash -ex
+
+exec docker buildx build --push \
+    --platform linux/amd64,linux/arm64,linux/ppc64le \
+    --build-arg http_proxy=$http_proxy \
+    -t docker.io/fnndsc/pl-fetal-surface-extract:base-1 .