enh: start lightweight FS installation

.github/workflows/docker-publish.yml

@@ -0,0 +1,72 @@
+
+name: Docker Image CI
+
+on:
+  push:
+    # Publish `main` as Docker `latest` image.
+    branches:
+      - main
+  release:
+    types: [published]
+
+  # Run tests for any PRs.
+  pull_request:
+
+env:
+  IMAGE_NAME: freesurfer
+
+jobs:
+  # Push image to GitHub Packages.
+  # See also https://docs.docker.com/docker-hub/builds/
+  push:
+    runs-on: ubuntu-latest
+    steps:
+      - uses: actions/checkout@v2
+
+      - name: Log into GitHub Container Registry
+        run: echo "${{ secrets.GH_PACKAGES_TOKEN }}" | docker login https://docker.pkg.github.com -u nipreps-bot --password-stdin
+
+      - uses: satackey/[email protected]
+        # Ignore the failure of a step and avoid terminating the job.
+        continue-on-error: true
+
+      - name: Build image
+        run: docker build . --file Dockerfile --tag $IMAGE_NAME
+
+      - name: Push image to GitHub Container Registry
+        if: github.event_name == 'release'
+        run: |
+          IMAGE_ID=docker.pkg.github.com/${{ github.repository }}/$IMAGE_NAME
+          # Change all uppercase to lowercase
+          IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
+          # Strip git ref prefix from version
+          VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
+          # Strip "v" prefix from tag name
+          [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
+          # Use Docker `latest` tag convention
+          [ "$VERSION" == "main" ] && VERSION=latest
+          echo IMAGE_ID=$IMAGE_ID
+          echo VERSION=$VERSION
+          docker tag $IMAGE_NAME $IMAGE_ID:$VERSION
+          docker push $IMAGE_ID:$VERSION
+
+      - name: Log into DockerHub Container Registry
+        run: echo "${{ secrets.DH_PAT }}" | docker login -u niprepsbot --password-stdin
+
+      - name: Push image to DockerHub Container Registry
+        if: github.event_name == 'release'
+        run: |
+          IMAGE_ID=nipreps/${IMAGE_NAME}
+          # Change all uppercase to lowercase
+          IMAGE_ID=$(echo $IMAGE_ID | tr '[A-Z]' '[a-z]')
+          # Strip git ref prefix from version
+          VERSION=$(echo "${{ github.ref }}" | sed -e 's,.*/\(.*\),\1,')
+          # Strip "v" prefix from tag name
+          [[ "${{ github.ref }}" == "refs/tags/"* ]] && VERSION=$(echo $VERSION | sed -e 's/^v//')
+          # Use Docker `latest` tag convention
+          [ "$VERSION" == "main" ] && VERSION=latest
+          echo IMAGE_ID=$IMAGE_ID
+          echo VERSION=$VERSION
+          docker tag $IMAGE_NAME $IMAGE_ID:$VERSION
+          docker push $IMAGE_ID:$VERSION
+

Dockerfile

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+# NiPreps lightweight image of FreeSurfer
+#
+# MIT License
+#
+# Copyright (c) 2021 The NiPreps Developers
+#
+# Permission is hereby granted, free of charge, to any person obtaining a copy
+# of this software and associated documentation files (the "Software"), to deal
+# in the Software without restriction, including without limitation the rights
+# to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+# copies of the Software, and to permit persons to whom the Software is
+# furnished to do so, subject to the following conditions:
+#
+# The above copyright notice and this permission notice shall be included in all
+# copies or substantial portions of the Software.
+#
+# THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+# IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+# FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+# AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+# LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+# OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+# SOFTWARE.
+
+# Use our miniconda base
+FROM alpine:3.15
+
+# Update
+RUN apk update && \
+    apk upgrade && \
+    apk add --update curl && \
+    apk add --no-cache tar gzip && \
+    rm -rf /var/cache/apk/*
+
+# Installing freesurfer
+RUN curl -sSL https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.1/freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.1.tar.gz \
+    | tar zxv --no-same-owner -C /opt \
+    --exclude='freesurfer/diffusion' \
+    --exclude='freesurfer/docs' \
+    --exclude='freesurfer/fsfast' \
+    --exclude='freesurfer/lib/cuda' \
+    --exclude='freesurfer/lib/qt' \
+    --exclude='freesurfer/matlab' \
+    --exclude='freesurfer/mni/share/man' \
+    --exclude='freesurfer/subjects/fsaverage_sym' \
+    --exclude='freesurfer/subjects/fsaverage3' \
+    --exclude='freesurfer/subjects/fsaverage4' \
+    --exclude='freesurfer/subjects/cvs_avg35' \
+    --exclude='freesurfer/subjects/cvs_avg35_inMNI152' \
+    --exclude='freesurfer/subjects/bert' \
+    --exclude='freesurfer/subjects/lh.EC_average' \
+    --exclude='freesurfer/subjects/rh.EC_average' \
+    --exclude='freesurfer/subjects/sample-*.mgz' \
+    --exclude='freesurfer/subjects/V1_average' \
+    --exclude='freesurfer/trctrain'
+