feat: add containers (#26)

* add dotfiles to gitignore * add build-and-push gh action per toolkit * add dockerfiles and install scripts * add launch scripts and def files for uppmax * add qmd docs for workshop * add readme for containers folder * rename containers docs qmd file * udpate readme with new image names
NBISweden · Dec 23, 2023 · 62fefa1 · 62fefa1
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diff --git a/.github/workflows/docker-publish-bioconductor-spatial.yaml b/.github/workflows/docker-publish-bioconductor-spatial.yaml
@@ -0,0 +1,67 @@
+name: Build and Push Bioconductor-Spatial
+
+on:
+  push:
+    branches: 
+      - "master"
+    paths:
+      - "containers/dockerfiles/bioconductor_spatial.Dockerfile"
+      - "containers/scripts/install_bioconductor_spatial.sh"
+      - "containers/scripts/reticulate_install_bioconductor_spatial.R"
+  workflow_dispatch:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+  IMAGE_TAG: 2023-bioconductor_spatial-r4.3.0
+
+
+jobs:
+  bioconductor_spatial:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Install cosign
+        uses: sigstore/cosign-installer@6e04d228eb30da1757ee4e1dd75a0ec73a653e06 #v3.1.1
+        with:
+          cosign-release: 'v2.1.1'
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
+
+      - name: Log into registry ${{ env.REGISTRY }}
+        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0
+        with:
+          context: ./containers
+          file: containers/dockerfiles/bioconductor_spatial.Dockerfile
+          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ env.IMAGE_TAG }}
+          labels: ${{ steps.meta.outputs.labels }}
+          push: true
+
+      - name: Sign the published Docker image
+        env:
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}
diff --git a/.github/workflows/docker-publish-bioconductor.yaml b/.github/workflows/docker-publish-bioconductor.yaml
@@ -0,0 +1,67 @@
+name: Build and Push Bioconductor
+
+on:
+  push:
+    branches: 
+      - "master"
+    paths:
+      - "containers/dockerfiles/bioconductor.Dockerfile"
+      - "containers/scripts/install_bioconductor.sh"
+      - "containers/scripts/reticulate_install_bioconductor.R"
+  workflow_dispatch:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+  IMAGE_TAG: 2023-bioconductor-r4.3.0
+
+
+jobs:
+  bioconductor:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Install cosign
+        uses: sigstore/cosign-installer@6e04d228eb30da1757ee4e1dd75a0ec73a653e06 #v3.1.1
+        with:
+          cosign-release: 'v2.1.1'
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
+
+      - name: Log into registry ${{ env.REGISTRY }}
+        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0
+        with:
+          context: ./containers
+          file: containers/dockerfiles/bioconductor.Dockerfile
+          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ env.IMAGE_TAG }}
+          labels: ${{ steps.meta.outputs.labels }}
+          push: true
+
+      - name: Sign the published Docker image
+        env:
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}
diff --git a/.github/workflows/docker-publish-scanpy-spatial.yaml b/.github/workflows/docker-publish-scanpy-spatial.yaml
@@ -0,0 +1,67 @@
+name: Build and Push Scanpy-Spatial
+
+on:
+  push:
+    branches: 
+      - "master"
+    paths:
+      - "containers/dockerfiles/scanpy_spatial.Dockerfile"
+      - "containers/scripts/install_scanpy_spatial.sh"
+      - "containers/scripts/reticulate_install_scanpy_spatial.R"
+  workflow_dispatch:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+  IMAGE_TAG: 2023-scanpy_spatial-py3.10
+
+
+jobs:
+  scanpy_spatial:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Install cosign
+        uses: sigstore/cosign-installer@6e04d228eb30da1757ee4e1dd75a0ec73a653e06 #v3.1.1
+        with:
+          cosign-release: 'v2.1.1'
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
+
+      - name: Log into registry ${{ env.REGISTRY }}
+        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0
+        with:
+          context: ./containers
+          file: containers/dockerfiles/scanpy_spatial.Dockerfile
+          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ env.IMAGE_TAG }}
+          labels: ${{ steps.meta.outputs.labels }}
+          push: true
+
+      - name: Sign the published Docker image
+        env:
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}
diff --git a/.github/workflows/docker-publish-scanpy.yaml b/.github/workflows/docker-publish-scanpy.yaml
@@ -0,0 +1,67 @@
+name: Build and Push Scanpy
+
+on:
+  push:
+    branches: 
+      - "master"
+    paths:
+      - "containers/dockerfiles/scanpy.Dockerfile"
+      - "containers/scripts/install_scanpy.sh"
+      - "containers/scripts/reticulate_install_scanpy.R"
+  workflow_dispatch:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+  IMAGE_TAG: 2023-scanpy-py3.10
+
+
+jobs:
+  scanpy:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Install cosign
+        uses: sigstore/cosign-installer@6e04d228eb30da1757ee4e1dd75a0ec73a653e06 #v3.1.1
+        with:
+          cosign-release: 'v2.1.1'
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
+
+      - name: Log into registry ${{ env.REGISTRY }}
+        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0
+        with:
+          context: ./containers
+          file: containers/dockerfiles/scanpy.Dockerfile
+          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ env.IMAGE_TAG }}
+          labels: ${{ steps.meta.outputs.labels }}
+          push: true
+
+      - name: Sign the published Docker image
+        env:
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}
diff --git a/.github/workflows/docker-publish-seurat-spatial.yaml b/.github/workflows/docker-publish-seurat-spatial.yaml
@@ -0,0 +1,67 @@
+name: Build and Push Seurat-Spatial
+
+on:
+  push:
+    branches: 
+      - "master"
+    paths:
+      - "containers/dockerfiles/seurat_spatial.Dockerfile"
+      - "containers/scripts/install_seurat_spatial.sh"
+      - "containers/scripts/reticulate_install_seurat_spatial.R"
+  workflow_dispatch:
+
+env:
+  REGISTRY: ghcr.io
+  IMAGE_NAME: ${{ github.repository }}
+  IMAGE_TAG: 2023-seurat_spatial-r4.3.0
+
+
+jobs:
+  seurat_spatial:
+
+    runs-on: ubuntu-latest
+    permissions:
+      contents: read
+      packages: write
+      id-token: write
+
+    steps:
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      - name: Install cosign
+        uses: sigstore/cosign-installer@6e04d228eb30da1757ee4e1dd75a0ec73a653e06 #v3.1.1
+        with:
+          cosign-release: 'v2.1.1'
+
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@f95db51fddba0c2d1ec667646a06c2ce06100226 # v3.0.0
+
+      - name: Log into registry ${{ env.REGISTRY }}
+        uses: docker/login-action@343f7c4344506bcbf9b4de18042ae17996df046d # v3.0.0
+        with:
+          registry: ${{ env.REGISTRY }}
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      - name: Extract Docker metadata
+        id: meta
+        uses: docker/metadata-action@96383f45573cb7f253c731d3b3ab81c87ef81934 # v5.0.0
+        with:
+          images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}
+
+      - name: Build and push Docker image
+        id: build-and-push
+        uses: docker/build-push-action@0565240e2d4ab88bba5387d719585280857ece09 # v5.0.0
+        with:
+          context: ./containers
+          file: containers/dockerfiles/seurat_spatial.Dockerfile
+          tags: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME }}:${{ env.IMAGE_TAG }}
+          labels: ${{ steps.meta.outputs.labels }}
+          push: true
+
+      - name: Sign the published Docker image
+        env:
+          TAGS: ${{ steps.meta.outputs.tags }}
+          DIGEST: ${{ steps.build-and-push.outputs.digest }}
+        run: echo "${TAGS}" | xargs -I {} cosign sign --yes {}@${DIGEST}