diff --git a/.github/workflows/build-base-extra.yaml b/.github/workflows/build-base-extra.yaml index 3279de8..5040e10 100644 --- a/.github/workflows/build-base-extra.yaml +++ b/.github/workflows/build-base-extra.yaml @@ -25,9 +25,12 @@ jobs: - uses: actions/checkout@master - name: Publish base-extra to Docker Hub uses: elgohr/Publish-Docker-Github-Action@master + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} with: name: facilebio/facilebio_base_extra username: ${{ secrets.DOCKER_USERNAME }} password: ${{ secrets.DOCKER_PASSWORD }} workdir: facilebio_base_extra + buildargs: GITHUB_PAT diff --git a/.github/workflows/build-base.yaml b/.github/workflows/build-base.yaml index 4a7f30c..375af3b 100644 --- a/.github/workflows/build-base.yaml +++ b/.github/workflows/build-base.yaml @@ -25,8 +25,11 @@ jobs: - uses: actions/checkout@master - name: Publish base to Docker Hub uses: elgohr/Publish-Docker-Github-Action@master + env: + GITHUB_PAT: ${{ secrets.GITHUB_TOKEN }} with: name: facilebio/facilebio_base username: ${{ secrets.DOCKER_USERNAME }} password: ${{ secrets.DOCKER_PASSWORD }} workdir: facilebio_base + buildargs: GITHUB_PAT diff --git a/.github/workflows/build-facielbio2.yaml b/.github/workflows/build-facielbio2.yaml new file mode 100644 index 0000000..b4def8c --- /dev/null +++ b/.github/workflows/build-facielbio2.yaml @@ -0,0 +1,55 @@ +# https://josephrodriguezg.medium.com/build-and-publish-docker-images-with-github-actions-78be3b3fbb9b +# https://github.com/docker/build-push-action +name: Build final facilebio image +on: + push: + branches: + - '*' + paths: + - 'facilebio/**' + schedule: + # https://help.github.com/en/actions/reference/workflow-syntax-for-github-actions#onschedule + # https://crontab.guru/ to debug cron syntax + # run monday's and thursdays (1,4) at 5:00 AM Pacific Time (which is noon UTC) + - cron: '0 12 * * 1,4' + workflow_dispatch: + inputs: + dummy: + description: 'A dummy variable to enable manual workflow execution' + required: false + default: 'gitty up' +jobs: + build: + name: Build & push docker image + runs-on: ubuntu-latest + env: + IMG_NAME: facilebio/facilebio + steps: + - name: Checkout + uses: actions/checkout@v4 + + - name: Debug + run: | + echo "GITHUB_TOKEN -> {{ secrets.GITHUB_TOKEN }}" + + - name: Docker metadata + id: metadata + uses: docker/metadata-action@v3 + with: + images: ${{ env.IMG_NAME }} + tags: | + type=ref,event=branch + + - name: Log in to Docker Hub + uses: docker/login-action@v1 + with: + username: ${{ secrets.DOCKER_USERNAME }} + password: ${{ secrets.DOCKER_PASSWORD }} + + - name: Build and push docker image + uses: docker/build-push-action@v5 + with: + push: true + tags: ${{ env.IMG_NAME }}:latest + context: facilebio + secret-envs: GITHUB_PAT={{ secrets.GITHUB_TOKEN }} diff --git a/facilebio_base/base-packages.txt b/facilebio_base/base-packages.txt index 047a3ac..d66132a 100644 --- a/facilebio_base/base-packages.txt +++ b/facilebio_base/base-packages.txt @@ -47,6 +47,7 @@ crayon crosstalk curl data.table +datamods DBI DESeq2 dbplyr @@ -169,6 +170,8 @@ qs R6 ragg rappdirs +reactable +reactR RBGL RColorBrewer RCurl @@ -195,6 +198,7 @@ S4Vectors scales shape shiny +shinybusy shinycssloaders shinydashboard shinydashboardPlus @@ -214,6 +218,7 @@ sva sys testthat tibble +tictoc tidyr tidyselect tinytex