adds SeqFu #1
Workflow file for this run
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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. ##### | |
| ##### ------------------------------------------------------------------------------------------------ ##### | |
| name: Update Freyja | |
| on: | |
| workflow_dispatch: | |
| schedule: | |
| - cron: '30 7 * * *' | |
| run-name: Updating Freyja | |
| jobs: | |
| update: | |
| runs-on: ubuntu-latest | |
| steps: | |
| # 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" >> $GITHUB_OUTPUT | |
| - name: pull repo | |
| uses: actions/checkout@v3 | |
| # Keeping here in case we want to figure out why this doesn't work | |
| # - name: get latest version of freyja in docker-builds repo | |
| # id: latest_version | |
| # run: | | |
| # file=$(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" >> $GITHUB_OUTPUT | |
| - name: set freyja version | |
| id: latest_version | |
| run: | | |
| version=1.4.8 | |
| echo "version=$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 | |
| - 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 | |
| - name: build to test | |
| id: docker_build_to_test | |
| uses: docker/build-push-action@v3 | |
| with: | |
| file: ${{ steps.latest_version.outputs.file }} | |
| target: test | |
| load: true | |
| push: false | |
| cache-from: type=local,src=/tmp/.buildx-cache-freyja | |
| cache-to: type=local,mode=max,dest=/tmp/.buildx-cache-freyja-new | |
| tags: freyja:update | |
| - name: get freyja database version | |
| id: db_version | |
| run: | | |
| docker run freyja:update freyja demix --version | |
| version=$(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 }} | |
| - name: Login to Quay | |
| uses: docker/login-action@v2 | |
| with: | |
| registry: quay.io | |
| username: ${{ secrets.QUAY_USERNAME }} | |
| password: ${{ secrets.QUAY_ROBOT_TOKEN }} | |
| - 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 }} | |
| - 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 }} | |
| - 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 |