Add a minimal user container for r2u/bioc2u repos (#1)

* Script for apt setup

* Add biocmanager

* Create user.Dockerfile

* Add matrix for builder/user

* Add matrix to merge

* Add type to digest

* Add curl

* Add install bspm and core

* Add ca-certificates

.github/workflows/build_ghcr.yaml

@@ -14,6 +14,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
+        type: [builder, user]
         ubuntu: [focal, jammy]
         platform: [linux/amd64]
 
@@ -26,7 +27,7 @@ jobs:
         id: meta
         uses: docker/metadata-action@v4
         with:
-          images: ghcr.io/${{ github.repository }}-builder
+          images: ghcr.io/${{ github.repository }}-${{ matrix.type }}
           tags: |
             type=raw,value=${{ matrix.ubuntu }}
 
@@ -59,7 +60,7 @@ jobs:
         with:
           build-args: |
             UBUNTU_TAG=${{matrix.ubuntu}}
-          file: builder.Dockerfile
+          file: ${{ matrix.type }}.Dockerfile
           labels: ${{ steps.meta.outputs.labels }}
           outputs: type=image,name=${{ steps.vars.outputs.container }},push-by-digest=true,name-canonical=true,push=true
           platforms: ${{matrix.platform}}
@@ -98,14 +99,14 @@ jobs:
       - name: Export digest by ubuntu and r versions
         run: |
           digest="${{ steps.build.outputs.digest }}"
-          mkdir -p /tmp/digests/${{matrix.ubuntu}}
-          touch "/tmp/digests/${{matrix.ubuntu}}/${digest#sha256:}"
-          mkdir -p /tmp/digests/${{matrix.ubuntu}}-r-${{steps.versions.outputs.rver}}
-          touch "/tmp/digests/${{matrix.ubuntu}}-r-${{steps.versions.outputs.rver}}/${digest#sha256:}"
-          mkdir -p /tmp/digests/${{steps.versions.outputs.osver}}
-          touch "/tmp/digests/${{steps.versions.outputs.osver}}/${digest#sha256:}"
-          mkdir -p /tmp/digests/${{steps.versions.outputs.osver}}-r-${{steps.versions.outputs.rver}}
-          touch "/tmp/digests/${{steps.versions.outputs.osver}}-r-${{steps.versions.outputs.rver}}/${digest#sha256:}"
+          mkdir -p /tmp/digests/${{matrix.type}}/${{matrix.ubuntu}}
+          touch "/tmp/digests/${{matrix.type}}/${{matrix.ubuntu}}/${digest#sha256:}"
+          mkdir -p /tmp/digests/${{matrix.type}}/${{matrix.ubuntu}}-r-${{steps.versions.outputs.rver}}
+          touch "/tmp/digests/${{matrix.type}}/${{matrix.ubuntu}}-r-${{steps.versions.outputs.rver}}/${digest#sha256:}"
+          mkdir -p /tmp/digests/${{matrix.type}}/${{steps.versions.outputs.osver}}
+          touch "/tmp/digests/${{matrix.type}}/${{steps.versions.outputs.osver}}/${digest#sha256:}"
+          mkdir -p /tmp/digests/${{matrix.type}}/${{steps.versions.outputs.osver}}-r-${{steps.versions.outputs.rver}}
+          touch "/tmp/digests/${{matrix.type}}/${{steps.versions.outputs.osver}}-r-${{steps.versions.outputs.rver}}/${digest#sha256:}"
 
       - name: Upload digests
         uses: actions/upload-artifact@v3
@@ -124,6 +125,7 @@ jobs:
       fail-fast: false
       matrix:
         ubuntu: [focal, jammy]
+        type: [builder, user]
     steps:
       - name: Download digests
         uses: actions/download-artifact@v3
@@ -147,7 +149,7 @@ jobs:
         id: meta
         uses: docker/metadata-action@v4
         with:
-          images: ghcr.io/${{ github.repository }}-builder
+          images: ghcr.io/${{ github.repository }}-${{ matrix.type }}
           tags: |
             type=raw,value=${{ matrix.ubuntu }}
 
@@ -158,6 +160,6 @@ jobs:
 
       - name: Create manifest list and push
         run: |
-          cd /tmp/digests
+          cd /tmp/digests/${{matrix.type}}
           ls --hide=digestdirs > digestdirs
           cat digestdirs | xargs -i bash -c 'docker buildx imagetools create -t ${{steps.vars.outputs.container}}:{} $(for f in {}/*; do basename "$f"; done | xargs printf "${{steps.vars.outputs.container}}@sha256:%s ")'

apt_setup.sh

@@ -0,0 +1,10 @@
+#!/bin/bash
+export UBUNTU_CODENAME=$(grep '^VERSION_CODENAME=' /etc/os-release | cut -d= -f2)
+apt update -qq
+apt install -y --no-install-recommends curl ca-certificates
+curl -O https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_$UBUNTU_CODENAME.sh
+bash add_cranapt_$UBUNTU_CODENAME.sh
+rm add_cranapt_$UBUNTU_CODENAME.sh
+echo "deb [trusted=yes] https://js2.jetstream-cloud.org:8001/swift/v1/bioc2u/ $UBUNTU_CODENAME release" | tee -a /etc/apt/sources.list.d/bioc2u.list > /dev/null
+apt update -qq
+DEBIAN_FRONTEND=noninteractive apt install -y r-base-core r-cran-biocmanager r-cran-bspm

user.Dockerfile

@@ -0,0 +1,7 @@
+ARG BASE_IMAGE=ubuntu
+ARG UBUNTU_TAG=jammy
+FROM ${BASE_IMAGE}:${UBUNTU_TAG} AS base
+
+USER root
+COPY apt_setup.sh /bioc_scripts/apt_setup.sh
+RUN bash /bioc_scripts/apt_setup.sh