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| ##### ------------------------------------------------------------------------------------------------ ##### | ||
| ##### This caller workflow tests, builds, and pushes the image to Docker Hub and Quay using the most ##### | ||
| ##### recent version of Freyja and downloading the most recent variant information. ##### | ||
| ##### It takes no manual input. ##### | ||
| ##### ------------------------------------------------------------------------------------------------ ##### | ||
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| name: Update Freyja | ||
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| on: | ||
| workflow_dispatch: | ||
| schedule: | ||
| - cron: '30 7 * * *' | ||
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| run-name: Updating Freyja | ||
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| jobs: | ||
| update: | ||
| runs-on: ubuntu-latest | ||
| steps: | ||
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| # Keeping here in case we want to use it to keep Freyja's version up-to-date as well | ||
| # - name: Get latest release | ||
| # uses: rez0n/actions-github-release@main | ||
| # id: latest_release | ||
| # with: | ||
| # token: ${{ secrets.GITHUB_TOKEN }} | ||
| # repository: andersen-lab/Freyja | ||
| # type: "stable" | ||
| # - name: Remove V | ||
| # id: strip | ||
| # run: | | ||
| # version=$(echo "${{ steps.latest_release.outputs.release }}" | sed 's/V//g' | sed 's/v//g' ) | ||
| # echo "The version is $version" | ||
| # echo "version=$version" >> $GITHUB_OUTPUT | ||
|
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| - name: pull repo | ||
| uses: actions/checkout@v3 | ||
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| # Keeping here in case we want to figure out why this doesn't work | ||
| # - name: get latest version of freyja in docker-builds repo | ||
| # id: latest_version | ||
| # run: | | ||
| # file=$(git log -1 --name-only --format=%cd --date=iso freyja/*/Dockerfile | grep Dockerfile | head -n 1 ) | ||
| # echo "the latest file is $file" | ||
| # echo "file=$file" >> $GITHUB_OUTPUT | ||
| # | ||
| # version=$(echo $file | cut -f 2 -d "/" | cut -f 1 -d "_") | ||
| # echo "the latest version is $version" | ||
| # echo "version=$version" >> $GITHUB_OUTPUT | ||
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| - name: set freyja version | ||
| id: latest_version | ||
| run: | | ||
| version=1.4.8 | ||
| echo "version=$version" >> $GITHUB_OUTPUT | ||
| file=freyja/$version/Dockerfile | ||
| ls $file | ||
| echo "file=$file" >> $GITHUB_OUTPUT | ||
| - name: set up docker buildx | ||
| id: buildx | ||
| uses: docker/setup-buildx-action@v2 | ||
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| - name: cache docker layers | ||
| uses: actions/cache@v3 | ||
| with: | ||
| path: /tmp/.buildx-cache-freyja | ||
| key: ${{ runner.os }}-buildx-freyja-${{ github.sha }} | ||
| restore-keys: ${{ runner.os }}-buildx-freyja | ||
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| - name: build to test | ||
| id: docker_build_to_test | ||
| uses: docker/build-push-action@v3 | ||
| with: | ||
| file: ${{ steps.latest_version.outputs.file }} | ||
| target: test | ||
| load: true | ||
| push: false | ||
| cache-from: type=local,src=/tmp/.buildx-cache-freyja | ||
| cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-freyja-new | ||
| tags: freyja:update | ||
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| - name: get freyja database version | ||
| id: db_version | ||
| run: | | ||
| docker run freyja:update freyja demix --version | ||
| version=$(docker run freyja:update freyja demix --version | grep . | grep -v Barcode | head -n 1) | ||
| echo "the latest version is $version" | ||
| echo "version=$version" >> $GITHUB_OUTPUT | ||
| - name: Get current date | ||
| id: date | ||
| run: | | ||
| date=$(date '+%Y-%m-%d') | ||
| echo "the date is $date" | ||
| echo "date=$date" >> $GITHUB_OUTPUT | ||
| - name: Login to DockerHub | ||
| uses: docker/login-action@v2 | ||
| with: | ||
| username: ${{ secrets.DOCKER_HUB_USERNAME }} | ||
| password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }} | ||
|
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| - name: Login to Quay | ||
| uses: docker/login-action@v2 | ||
| with: | ||
| registry: quay.io | ||
| username: ${{ secrets.QUAY_USERNAME }} | ||
| password: ${{ secrets.QUAY_PASSWORD }} | ||
|
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| - name: Build and push user-defined tag to DockerHub | ||
| id: docker_build_user_defined_tag | ||
| uses: docker/build-push-action@v3 | ||
| with: | ||
| file: ${{ steps.latest_version.outputs.file }} | ||
| target: app | ||
| push: true | ||
| cache-from: type=local,src=/tmp/.buildx-cache-freyja | ||
| cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-freyja-new # mode=max means export layers from all stage to cache | ||
| tags: staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }} | ||
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| - name: Build and push to Quay | ||
| id: build | ||
| uses: docker/build-push-action@v3 | ||
| with: | ||
| file: ${{ steps.latest_version.outputs.file }} | ||
| target: app | ||
| push: true | ||
| cache-from: type=local,src=/tmp/.buildx-cache-freyja | ||
| cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-freyja-new # mode=max means export | ||
| tags: quay.io/staphb/freyja:${{ steps.latest_version.outputs.version }}-${{ steps.db_version.outputs.version }}-${{ steps.date.outputs.date }} | ||
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| - name: Move cache # apparently prevents the cache from growing in size forever | ||
| run: | | ||
| rm -rf /tmp/.buildx-cache-freyja | ||
| mv /tmp/.buildx-cache-freyja-new /tmp/.buildx-cache-freyja | ||
| - name: Image digest | ||
| run: echo ${{ steps.docker_build.outputs.digest }} |
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