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Add NVIDIA base containers (#139)
* Flexible base image * Try matrix with Nvidia base * Update build_ghcr.yaml * Update Dockerfile * Try named prefix * Fix named prefix * Add dash to OS version * Try squash with nvidia --------- Co-authored-by: jwokaty <[email protected]>
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‎.github/workflows/build_ghcr.yaml‎

Lines changed: 27 additions & 20 deletions
Original file line numberDiff line numberDiff line change
@@ -15,9 +15,11 @@ jobs:
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strategy:
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fail-fast: false
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matrix:
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ubuntu: [noble]
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platform: [linux/amd64]
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branch: [devel, release]
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base:
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- {image: "ubuntu:noble", name: "noble"}
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- {image: "nvcr.io/nvidia/cuda:12.9.0-devel-ubuntu24.04", name: "nvidia-noble"}
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name: Build container images for GHCR
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runs-on: ubuntu-latest
@@ -35,7 +37,7 @@ jobs:
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with:
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images: ghcr.io/${{ github.repository }}
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tags: |
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type=raw,value=${{ matrix.ubuntu }}
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type=raw,value=${{ matrix.base.name }}
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- name: Extract container name without tag
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id: vars
@@ -64,16 +66,18 @@ jobs:
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id: build
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uses: docker/build-push-action@v5
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with:
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build-args: CYCLE=${{matrix.branch}}
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build-args: |
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CYCLE=${{matrix.branch}}
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BASE_IMAGE=${{matrix.base.image}}
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labels: ${{ steps.meta.outputs.labels }}
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outputs: type=image,name=${{ steps.vars.outputs.container }},push-by-digest=true,name-canonical=true,push=true
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platforms: ${{matrix.platform}}
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provenance: false
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- name: Prepare Dockerfile to extract R version with emulator
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run: |
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mkdir -p ${{matrix.ubuntu}}-${{matrix.platform}}
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cat << "EOF" > ${{matrix.ubuntu}}-${{matrix.platform}}-r.Dockerfile
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mkdir -p ${{matrix.base.image}}-${{matrix.platform}}
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cat << "EOF" > ${{matrix.base.image}}-${{matrix.platform}}-r.Dockerfile
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FROM ${{ steps.vars.outputs.container }}@${{ steps.build.outputs.digest }} as extract
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USER root
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RUN mkdir /bioctmp && /bbs_r_start -e 'BiocManager::version()' | grep '\[1\]' | awk -F"'" '{print $2}' > /bioctmp/biocver && /bbs_r_start --slave -e 'cat(paste(version$major, version$minor, sep = "."))' > /bioctmp/rver && cat /etc/os-release > /bioctmp/os-release
@@ -84,26 +88,29 @@ jobs:
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- name: Build and push container image to ghcr
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uses: docker/build-push-action@v5
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with:
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file: ${{matrix.ubuntu}}-${{matrix.platform}}-r.Dockerfile
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file: ${{matrix.base.image}}-${{matrix.platform}}-r.Dockerfile
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context: .
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push: false
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load: false
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provenance: false
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outputs: type=tar,dest=${{matrix.ubuntu}}-${{matrix.platform}}/r.tar
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outputs: type=tar,dest=${{matrix.base.image}}-${{matrix.platform}}/r.tar
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tags: ${{ steps.meta.outputs.tags }}-r
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platforms: ${{ matrix.platform }}
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- name: Extract rversion
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id: versions
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run: |
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cd ${{matrix.ubuntu}}-${{matrix.platform}}
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cd ${{matrix.base.image}}-${{matrix.platform}}
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tar -xvf r.tar
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echo rver=$(cat rver) >> $GITHUB_OUTPUT
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echo biocver=$(cat biocver) >> $GITHUB_OUTPUT
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echo osver=$(awk -F= '/VERSION_ID/ {gsub("\"", "", $2); print $2}' os-release) >> $GITHUB_OUTPUT
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BASEPREFIX=""
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if [ '${{matrix.branch}}' == 'devel' ]; then BASEPREFIX="devel-"; fi
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NAMEDPREFIX="${BASEPREFIX}${{matrix.base.name}}"
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BASEPREFIX=$(echo "$NAMEDPREFIX" | sed 's/-\?jammy//')
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echo baseprefix=$BASEPREFIX >> $GITHUB_OUTPUT
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echo namedprefix=$NAMEDPREFIX >> $GITHUB_OUTPUT
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- name: Export digest by ubuntu and r versions
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run: |
@@ -115,18 +122,18 @@ jobs:
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exit 1
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fi
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digest="${{ steps.build.outputs.digest }}"
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mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}${{matrix.ubuntu}}
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touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}${{matrix.ubuntu}}/${digest#sha256:}"
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mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}${{matrix.ubuntu}}-bioc-${{steps.versions.outputs.biocver}}
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touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}${{matrix.ubuntu}}-bioc-${{steps.versions.outputs.biocver}}/${digest#sha256:}"
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mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}${{matrix.ubuntu}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}}
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touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}${{matrix.ubuntu}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}}/${digest#sha256:}"
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mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}${{steps.versions.outputs.osver}}
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touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}${{steps.versions.outputs.osver}}/${digest#sha256:}"
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mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}
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touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}/${digest#sha256:}"
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mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}}
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touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}}/${digest#sha256:}"
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mkdir -p /tmp/digests/${{steps.versions.outputs.namedprefix}}
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touch "/tmp/digests/${{steps.versions.outputs.namedprefix}}/${digest#sha256:}"
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mkdir -p /tmp/digests/${{steps.versions.outputs.namedprefix}}-bioc-${{steps.versions.outputs.biocver}}
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touch "/tmp/digests/${{steps.versions.outputs.namedprefix}}-bioc-${{steps.versions.outputs.biocver}}/${digest#sha256:}"
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mkdir -p /tmp/digests/${{steps.versions.outputs.namedprefix}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}}
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touch "/tmp/digests/${{steps.versions.outputs.namedprefix}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}}/${digest#sha256:}"
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mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}-${{steps.versions.outputs.osver}}
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touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}-${{steps.versions.outputs.osver}}/${digest#sha256:}"
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mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}-${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}
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touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}-${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}/${digest#sha256:}"
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mkdir -p /tmp/digests/${{steps.versions.outputs.baseprefix}}-${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}}
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touch "/tmp/digests/${{steps.versions.outputs.baseprefix}}-${{steps.versions.outputs.osver}}-bioc-${{steps.versions.outputs.biocver}}-r-${{steps.versions.outputs.rver}}/${digest#sha256:}"
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- name: Upload digests
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uses: actions/upload-artifact@v4

‎Dockerfile‎

Lines changed: 3 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1,12 +1,13 @@
1-
FROM ubuntu:noble AS build
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ARG BASE_IMAGE=ubuntu:noble
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FROM ${BASE_IMAGE} AS build
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ARG CYCLE=release
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RUN useradd -ms /bin/bash biocbuild && apt update -qq && apt install sudo systemd -y && usermod -aG sudo biocbuild && echo "biocbuild ALL=(ALL) NOPASSWD:ALL" >> /etc/sudoers
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USER biocbuild
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COPY . /home/biocbuild/bioconductor_salt
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WORKDIR /home/biocbuild
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RUN DEBIAN_FRONTEND="noninteractive" bash bioconductor_salt/startup_bbs_standalone_${CYCLE}.sh
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9-
FROM ubuntu:noble AS final
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FROM ${BASE_IMAGE AS final
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COPY --from=build / /
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ENTRYPOINT ["/bin/bash", "-c"]
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CMD ["/bbs_r_start"]

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