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daily-rocker-builds.yaml
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name: Extra rocker builds
on:
workflow_dispatch:
inputs:
rver:
default: "devel"
biocver:
default: "3.18"
schedule:
- cron: '0 18 * * *'
jobs:
buildrver:
strategy:
matrix:
arch: [amd64, arm64]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Free root space
uses: almahmoud/free-root-space@main
with:
verbose: true
- name: Set defaults for schedule
id: defs
run: |
echo rver=$(echo ${{ github.event.inputs.rver || 'devel' }}) >> $GITHUB_OUTPUT
echo biocver=$(echo ${{ github.event.inputs.biocver || '3.18' }}) >> $GITHUB_OUTPUT
echo registryuser=$(echo ${{ github.repository_owner }} | awk '{print tolower($0)}') >> $GITHUB_OUTPUT
echo rockerintermediateprefix=$(echo "ghcr.io/${{ github.repository_owner }}/rocker" | awk '{print tolower($0)}') >> $GITHUB_OUTPUT
- name: Set up QEMU
uses: docker/setup-qemu-action@v2
with:
platforms: arm64
if: matrix.arch == 'arm64'
- name: Login to GHCR
uses: docker/login-action@v2
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Prep rocker rocker files
run: bash .github/scripts/rocker_prep.sh ${{ steps.defs.outputs.rver }} ${{ steps.defs.outputs.biocver }} ${{ steps.defs.outputs.rockerintermediateprefix }} ${{ matrix.arch }}
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
with:
platforms: linux/${{ matrix.arch }}
- name: Build and push r-ver
uses: docker/build-push-action@v3
with:
file: rocker-versioned2/dockerfiles/r-ver_${{ steps.defs.outputs.rver }}.Dockerfile
context: rocker-versioned2
push: true
tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-r-ver:${{ steps.defs.outputs.rver }}-${{ matrix.arch }}
platforms: linux/${{ matrix.arch }}
buildrstudio:
strategy:
matrix:
arch: [amd64, arm64]
needs: buildrver
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Free root space
uses: almahmoud/free-root-space@main
with:
verbose: true
- name: Set defaults for schedule
id: defs
run: |
echo rver=$(echo ${{ github.event.inputs.rver || 'devel' }}) >> $GITHUB_OUTPUT
echo biocver=$(echo ${{ github.event.inputs.biocver || '3.18' }}) >> $GITHUB_OUTPUT
echo registryuser=$(echo ${{ github.repository_owner }} | awk '{print tolower($0)}') >> $GITHUB_OUTPUT
echo rockerintermediateprefix=$(echo "ghcr.io/${{ github.repository_owner }}/rocker" | awk '{print tolower($0)}') >> $GITHUB_OUTPUT
- name: Set up QEMU
uses: docker/setup-qemu-action@v2
with:
platforms: arm64
if: matrix.arch == 'arm64'
- name: Login to GHCR
uses: docker/login-action@v2
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Prep rocker rocker files
run: |
bash .github/scripts/rocker_prep.sh ${{ steps.defs.outputs.rver }} ${{ steps.defs.outputs.biocver }} ${{ steps.defs.outputs.rockerintermediateprefix }} ${{ matrix.arch }}
- name: Move some tidyverse builds to docker for arm64 to avoid timeout
run: |
head -n44 rocker-versioned2/scripts/install_tidyverse.sh >> rocker-versioned2/scripts/install_rstudio.sh
sed -i "\|RUN /rocker_scripts/install_rstudio.sh|i COPY scripts /rocker_scripts" rocker-versioned2/dockerfiles/rstudio_${{ steps.defs.outputs.rver }}.Dockerfile
if: matrix.arch == 'arm64'
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
with:
platforms: linux/${{ matrix.arch }}
- name: Build and push rstudio
uses: docker/build-push-action@v3
with:
file: rocker-versioned2/dockerfiles/rstudio_${{ steps.defs.outputs.rver }}.Dockerfile
context: rocker-versioned2
push: true
tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-rstudio:${{ steps.defs.outputs.rver }}-${{ matrix.arch }}
platforms: linux/${{ matrix.arch }}
buildtidyverse:
strategy:
matrix:
arch: [amd64, arm64]
runs-on: ubuntu-latest
needs: buildrstudio
steps:
- uses: actions/checkout@v3
- name: Free root space
uses: almahmoud/free-root-space@main
with:
verbose: true
- name: Set defaults for schedule
id: defs
run: |
echo rver=$(echo ${{ github.event.inputs.rver || 'devel' }}) >> $GITHUB_OUTPUT
echo biocver=$(echo ${{ github.event.inputs.biocver || '3.18' }}) >> $GITHUB_OUTPUT
echo registryuser=$(echo ${{ github.repository_owner }} | awk '{print tolower($0)}') >> $GITHUB_OUTPUT
echo rockerintermediateprefix=$(echo "ghcr.io/${{ github.repository_owner }}/rocker" | awk '{print tolower($0)}') >> $GITHUB_OUTPUT
- name: Set up QEMU
uses: docker/setup-qemu-action@v2
with:
platforms: arm64
if: matrix.arch == 'arm64'
- name: Login to GHCR
uses: docker/login-action@v2
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Prep rocker rocker files
run: bash .github/scripts/rocker_prep.sh ${{ steps.defs.outputs.rver }} ${{ steps.defs.outputs.biocver }} ${{ steps.defs.outputs.rockerintermediateprefix }} ${{ matrix.arch }}
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
with:
platforms: linux/${{ matrix.arch }}
- name: Build and push tidyverse
uses: docker/build-push-action@v3
with:
file: rocker-versioned2/dockerfiles/tidyverse_${{ steps.defs.outputs.rver }}.Dockerfile
context: rocker-versioned2
push: true
tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-tidyverse:${{ steps.defs.outputs.rver }}-${{ matrix.arch }}
platforms: linux/${{ matrix.arch }}
mlbuild:
strategy:
matrix:
arch: [amd64]
runs-on: ubuntu-latest
steps:
- uses: actions/checkout@v3
- name: Free root space
uses: almahmoud/free-root-space@main
with:
verbose: true
- name: Set defaults for schedule
id: defs
run: |
echo rver=$(echo ${{ github.event.inputs.rver || 'devel' }}) >> $GITHUB_OUTPUT
echo biocver=$(echo ${{ github.event.inputs.biocver || '3.18' }}) >> $GITHUB_OUTPUT
echo registryuser=$(echo ${{ github.repository_owner }} | awk '{print tolower($0)}') >> $GITHUB_OUTPUT
echo rockerintermediateprefix=$(echo "ghcr.io/${{ github.repository_owner }}/rocker" | awk '{print tolower($0)}') >> $GITHUB_OUTPUT
- name: Set up QEMU
uses: docker/setup-qemu-action@v2
with:
platforms: arm64
if: matrix.arch == 'arm64'
- name: Login to GHCR
uses: docker/login-action@v2
with:
registry: ghcr.io
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Prep rocker rocker files
run: |
## git clone rocker
git clone --depth 1 https://github.com/rocker-org/rocker-versioned2
sed -i 's#rocker/cuda:${{ steps.defs.outputs.rver }}#${{ steps.defs.outputs.rockerintermediateprefix }}-cuda:${{ steps.defs.outputs.rver }}-${{ matrix.arch }}#g' rocker-versioned2/dockerfiles/ml_${{ steps.defs.outputs.rver }}.Dockerfile
sed -i 's#rocker/ml:${{ steps.defs.outputs.rver }}#${{ steps.defs.outputs.rockerintermediateprefix }}-ml:${{ steps.defs.outputs.rver }}-${{ matrix.arch }}#g' rocker-versioned2/dockerfiles/ml-verse_${{ steps.defs.outputs.rver }}.Dockerfile
BIOC_MINOR=$(echo "${{ steps.defs.outputs.biocver }}" | awk -F'.' '{print $NF}')
echo "Bioconductor Version: ${{ steps.defs.outputs.biocver }}"
if [ "${{ steps.defs.outputs.rver }}" = "devel" ];
then
if [ $((BIOC_MINOR%2)) -eq 0 ];
then
echo "Using latest release R since Bioc devel version is even";
sed -i 's#R_VERSION=${{ steps.defs.outputs.rver }}#R_VERSION=latest#g' rocker-versioned2/dockerfiles/cuda_${{ steps.defs.outputs.rver }}.Dockerfile
else
echo "Using latest pre-release R since Bioc devel version is even";
sed -i 's#R_VERSION=${{ steps.defs.outputs.rver }}#R_VERSION=patched#g' rocker-versioned2/dockerfiles/cuda_${{ steps.defs.outputs.rver }}.Dockerfile
fi
fi
- name: Set up Docker Buildx
uses: docker/setup-buildx-action@v2
with:
platforms: linux/${{ matrix.arch }}
- name: Build and load cuda
uses: docker/build-push-action@v3
with:
file: rocker-versioned2/dockerfiles/cuda_${{ steps.defs.outputs.rver }}.Dockerfile
context: rocker-versioned2
push: true
tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-cuda:${{ steps.defs.outputs.rver }}-${{ matrix.arch }}
platforms: linux/${{ matrix.arch }}
- name: Build and load ml
uses: docker/build-push-action@v3
with:
file: rocker-versioned2/dockerfiles/ml_${{ steps.defs.outputs.rver }}.Dockerfile
context: rocker-versioned2
push: true
tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-ml:${{ steps.defs.outputs.rver }}-${{ matrix.arch }}
platforms: linux/${{ matrix.arch }}
- name: Build and load ml-verse
uses: docker/build-push-action@v3
with:
file: rocker-versioned2/dockerfiles/ml-verse_${{ steps.defs.outputs.rver }}.Dockerfile
context: rocker-versioned2
push: true
tags: ${{ steps.defs.outputs.rockerintermediateprefix }}-ml-verse:${{ steps.defs.outputs.rver }}-${{ matrix.arch }}
platforms: linux/${{ matrix.arch }}