From 199ad74efaefb7db47624a5e952b255ff2c0c8b1 Mon Sep 17 00:00:00 2001 From: Jeremy Date: Thu, 21 Aug 2025 08:35:44 -0700 Subject: [PATCH 1/2] Workflows: Removed old docs auto push. Added/renamed Docker images, removed cptac --- .github/workflows/build.yml | 178 ++++++++++++++++++++++++++++++------ .github/workflows/main.yml | 88 +++++++++--------- 2 files changed, 193 insertions(+), 73 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 2ee99176..f44de138 100755 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -25,7 +25,7 @@ jobs: - name: Build and push broad sanger omics uses: docker/build-push-action@v3 with: - file: ./build/docker/Dockerfile.broad_sanger_omics + file: ./coderbuild/docker/Dockerfile.broad_sanger_omics tags: | sgosline/broad-sanger-omics:latest sgosline/broad-sanger-omics:${{ github.ref_name }} @@ -49,7 +49,7 @@ jobs: - name: Build and push broad sanger experiment uses: docker/build-push-action@v3 with: - file: ./build/docker/Dockerfile.broad_sanger_exp + file: ./coderbuild/docker/Dockerfile.broad_sanger_exp tags: | sgosline/broad-sanger-exp:latest sgosline/broad-sanger-exp:${{ github.ref_name }} @@ -74,7 +74,7 @@ jobs: - name: Build and push genes uses: docker/build-push-action@v3 with: - file: ./build/docker/Dockerfile.genes + file: ./coderbuild/docker/Dockerfile.genes tags: | sgosline/genes:latest sgosline/genes:${{ github.ref_name }} @@ -98,14 +98,38 @@ jobs: - name: Build and push hcmi uses: docker/build-push-action@v3 with: - file: ./build/docker/Dockerfile.hcmi + file: ./coderbuild/docker/Dockerfile.hcmi tags: | sgosline/hcmi:latest sgosline/hcmi:${{ github.ref_name }} push: true platforms: linux/amd64 - build-cptac: + # build-cptac: + # runs-on: ubuntu-latest + # steps: + # - name: Checkout + # uses: actions/checkout@v3 + # - name: Set up QEMU + # uses: docker/setup-qemu-action@v3 + # - name: Set up Docker Buildx + # uses: docker/setup-buildx-action@v3 + # - name: Login to DockerHub + # uses: docker/login-action@v3 + # with: + # username: ${{ secrets.DOCKERHUB_USERNAME }} + # password: ${{ secrets.DOCKERHUB_PASSWORD }} + # - name: Build and push cptac + # uses: docker/build-push-action@v3 + # with: + # file: ./coderbuild/docker/Dockerfile.cptac + # tags: | + # sgosline/cptac:latest + # sgosline/cptac:${{ github.ref_name }} + # push: true + # platforms: linux/amd64 + + build-mpnst: runs-on: ubuntu-latest steps: - name: Checkout @@ -119,17 +143,17 @@ jobs: with: username: ${{ secrets.DOCKERHUB_USERNAME }} password: ${{ secrets.DOCKERHUB_PASSWORD }} - - name: Build and push cptac + - name: Build and push mpnst uses: docker/build-push-action@v3 with: - file: ./build/docker/Dockerfile.cptac + file: ./coderbuild/docker/Dockerfile.mpnst tags: | - sgosline/cptac:latest - sgosline/cptac:${{ github.ref_name }} + sgosline/mpnst:latest + sgosline/mpnst:${{ github.ref_name }} push: true platforms: linux/amd64 - build-mpnst: + build-beataml: runs-on: ubuntu-latest steps: - name: Checkout @@ -143,17 +167,17 @@ jobs: with: username: ${{ secrets.DOCKERHUB_USERNAME }} password: ${{ secrets.DOCKERHUB_PASSWORD }} - - name: Build and push mpnst + - name: Build and push beataml uses: docker/build-push-action@v3 with: - file: ./build/docker/Dockerfile.mpnst + file: ./coderbuild/docker/Dockerfile.beataml tags: | - sgosline/mpnst:latest - sgosline/mpnst:${{ github.ref_name }} + sgosline/beataml:latest + sgosline/beataml:${{ github.ref_name }} push: true platforms: linux/amd64 - build-beataml: + build-pancreatic: runs-on: ubuntu-latest steps: - name: Checkout @@ -167,17 +191,17 @@ jobs: with: username: ${{ secrets.DOCKERHUB_USERNAME }} password: ${{ secrets.DOCKERHUB_PASSWORD }} - - name: Build and push beataml + - name: Build and push pancreatic uses: docker/build-push-action@v3 with: - file: ./build/docker/Dockerfile.beataml + file: ./coderbuild/docker/Dockerfile.pancreatic tags: | - sgosline/beataml:latest - sgosline/beataml:${{ github.ref_name }} + sgosline/pancreatic:latest + sgosline/pancreatic:${{ github.ref_name }} push: true platforms: linux/amd64 - build-pancpdo: + build-upload: runs-on: ubuntu-latest steps: - name: Checkout @@ -191,17 +215,17 @@ jobs: with: username: ${{ secrets.DOCKERHUB_USERNAME }} password: ${{ secrets.DOCKERHUB_PASSWORD }} - - name: Build and push pancpdo + - name: Build and push upload uses: docker/build-push-action@v3 with: - file: ./build/docker/Dockerfile.pancpdo + file: ./coderbuild/docker/Dockerfile.upload tags: | - sgosline/pancpdo:latest - sgosline/pancpdo:${{ github.ref_name }} + sgosline/upload:latest + sgosline/upload:${{ github.ref_name }} push: true platforms: linux/amd64 - build-upload: + build-sarcoma: runs-on: ubuntu-latest steps: - name: Checkout @@ -215,12 +239,108 @@ jobs: with: username: ${{ secrets.DOCKERHUB_USERNAME }} password: ${{ secrets.DOCKERHUB_PASSWORD }} - - name: Build and push upload + - name: Build and push sarcoma uses: docker/build-push-action@v3 with: - file: ./build/docker/Dockerfile.upload + file: ./coderbuild/docker/Dockerfile.sarcoma tags: | - sgosline/upload:latest - sgosline/upload:${{ github.ref_name }} + sgosline/sarcoma:latest + sgosline/sarcoma:${{ github.ref_name }} + push: true + platforms: linux/amd64 + + build-liver: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v3 + - name: Set up QEMU + uses: docker/setup-qemu-action@v3 + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v3 + - name: Login to DockerHub + uses: docker/login-action@v3 + with: + username: ${{ secrets.DOCKERHUB_USERNAME }} + password: ${{ secrets.DOCKERHUB_PASSWORD }} + - name: Build and push liver + uses: docker/build-push-action@v3 + with: + file: ./coderbuild/docker/Dockerfile.liver + tags: | + sgosline/liver:latest + sgosline/liver:${{ github.ref_name }} + push: true + platforms: linux/amd64 + + build-bladder: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v3 + - name: Set up QEMU + uses: docker/setup-qemu-action@v3 + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v3 + - name: Login to DockerHub + uses: docker/login-action@v3 + with: + username: ${{ secrets.DOCKERHUB_USERNAME }} + password: ${{ secrets.DOCKERHUB_PASSWORD }} + - name: Build and push bladder + uses: docker/build-push-action@v3 + with: + file: ./coderbuild/docker/Dockerfile.bladder + tags: | + sgosline/bladder:latest + sgosline/bladder:${{ github.ref_name }} + push: true + platforms: linux/amd64 + + build-colorectal: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v3 + - name: Set up QEMU + uses: docker/setup-qemu-action@v3 + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v3 + - name: Login to DockerHub + uses: docker/login-action@v3 + with: + username: ${{ secrets.DOCKERHUB_USERNAME }} + password: ${{ secrets.DOCKERHUB_PASSWORD }} + - name: Build and push colorectal + uses: docker/build-push-action@v3 + with: + file: ./coderbuild/docker/Dockerfile.colorectal + tags: | + sgosline/colorectal:latest + sgosline/colorectal:${{ github.ref_name }} push: true platforms: linux/amd64 + + build-novartis: + runs-on: ubuntu-latest + steps: + - name: Checkout + uses: actions/checkout@v3 + - name: Set up QEMU + uses: docker/setup-qemu-action@v3 + - name: Set up Docker Buildx + uses: docker/setup-buildx-action@v3 + - name: Login to DockerHub + uses: docker/login-action@v3 + with: + username: ${{ secrets.DOCKERHUB_USERNAME }} + password: ${{ secrets.DOCKERHUB_PASSWORD }} + - name: Build and push novartis + uses: docker/build-push-action@v3 + with: + file: ./coderbuild/docker/Dockerfile.novartis + tags: | + sgosline/novartis:latest + sgosline/novartis:${{ github.ref_name }} + push: true + platforms: linux/amd64 \ No newline at end of file diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index ab600c2d..e51759f3 100755 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -1,48 +1,48 @@ -name: Docs +# name: Docs -on: - push: - tags: - - '*' # Triggers the workflow only on version tags - workflow_dispatch: # Allows manual triggering of the workflow +# on: +# push: +# tags: +# - '*' # Triggers the workflow only on version tags +# workflow_dispatch: # Allows manual triggering of the workflow -# Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages -permissions: - contents: write - pages: write - id-token: write +# # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages +# permissions: +# contents: write +# pages: write +# id-token: write -jobs: -# Placeholder - build-docs: - if: github.actor != 'github-actions[bot]' - # needs: [data-visualization-save-to-docs, upload-to-figshare, gen-stats-and-push] - runs-on: ubuntu-latest - steps: - - name: Checkout - uses: actions/checkout@v4 - - name: Setup Pages - uses: actions/configure-pages@v4 - - name: List files cwd - run: ls -lah - - name: List files with wildcard - run: ls -lah * - - name: Build with Jekyll - uses: actions/jekyll-build-pages@v1 - with: - source: ./docs - destination: ./_site - - name: Upload artifact - uses: actions/upload-pages-artifact@v3 +# jobs: +# # Placeholder +# build-docs: +# if: github.actor != 'github-actions[bot]' +# # needs: [data-visualization-save-to-docs, upload-to-figshare, gen-stats-and-push] +# runs-on: ubuntu-latest +# steps: +# - name: Checkout +# uses: actions/checkout@v4 +# - name: Setup Pages +# uses: actions/configure-pages@v4 +# - name: List files cwd +# run: ls -lah +# - name: List files with wildcard +# run: ls -lah * +# - name: Build with Jekyll +# uses: actions/jekyll-build-pages@v1 +# with: +# source: ./docs +# destination: ./_site +# - name: Upload artifact +# uses: actions/upload-pages-artifact@v3 - deploy-docs: - if: github.actor != 'github-actions[bot]' - needs: [build-docs] - environment: - name: github-pages - url: ${{ steps.deployment.outputs.page_url }} - runs-on: ubuntu-latest - steps: - - name: Deploy to GitHub Pages - id: deployment - uses: actions/deploy-pages@v4 \ No newline at end of file +# deploy-docs: +# if: github.actor != 'github-actions[bot]' +# needs: [build-docs] +# environment: +# name: github-pages +# url: ${{ steps.deployment.outputs.page_url }} +# runs-on: ubuntu-latest +# steps: +# - name: Deploy to GitHub Pages +# id: deployment +# uses: actions/deploy-pages@v4 \ No newline at end of file From e37f13e7b857a7f8bab96cb5a7f83f1237fab785 Mon Sep 17 00:00:00 2001 From: Jeremy Date: Thu, 21 Aug 2025 08:40:46 -0700 Subject: [PATCH 2/2] fully removed the workflow --- .github/workflows/main.yml | 48 -------------------------------------- 1 file changed, 48 deletions(-) delete mode 100755 .github/workflows/main.yml diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml deleted file mode 100755 index e51759f3..00000000 --- a/.github/workflows/main.yml +++ /dev/null @@ -1,48 +0,0 @@ -# name: Docs - -# on: -# push: -# tags: -# - '*' # Triggers the workflow only on version tags -# workflow_dispatch: # Allows manual triggering of the workflow - -# # Sets permissions of the GITHUB_TOKEN to allow deployment to GitHub Pages -# permissions: -# contents: write -# pages: write -# id-token: write - -# jobs: -# # Placeholder -# build-docs: -# if: github.actor != 'github-actions[bot]' -# # needs: [data-visualization-save-to-docs, upload-to-figshare, gen-stats-and-push] -# runs-on: ubuntu-latest -# steps: -# - name: Checkout -# uses: actions/checkout@v4 -# - name: Setup Pages -# uses: actions/configure-pages@v4 -# - name: List files cwd -# run: ls -lah -# - name: List files with wildcard -# run: ls -lah * -# - name: Build with Jekyll -# uses: actions/jekyll-build-pages@v1 -# with: -# source: ./docs -# destination: ./_site -# - name: Upload artifact -# uses: actions/upload-pages-artifact@v3 - -# deploy-docs: -# if: github.actor != 'github-actions[bot]' -# needs: [build-docs] -# environment: -# name: github-pages -# url: ${{ steps.deployment.outputs.page_url }} -# runs-on: ubuntu-latest -# steps: -# - name: Deploy to GitHub Pages -# id: deployment -# uses: actions/deploy-pages@v4 \ No newline at end of file