Merge pull request #116 from rasools/OMICSINT_H24

Add workflow for making docker images

.github/workflows/Build and Push Docker Images for Labs.yml

@@ -0,0 +1,115 @@
+name: Build and Push Docker Images for Labs
+
+on:
+  push:
+    paths:
+      - 'session_ml/DeepLearningDataIntegration/**'
+      - 'session_ml/FeatureSelectionIntegrOMICs/**'
+      - 'session_ml/SingleCell/**'
+      - 'session_gems/**'
+    branches:
+      - OMICSINT_H24
+
+jobs:
+  build:
+    runs-on: ubuntu-latest
+
+    if: github.repository == 'NBISweden/workshop_omics_integration'
+
+    steps:
+      # Checkout the repository
+      - name: Checkout repository
+        uses: actions/checkout@v3
+
+      # Set up Docker Buildx for multi-platform builds
+      - name: Set up Docker Buildx
+        uses: docker/setup-buildx-action@v2
+
+      # Log in to Docker Hub
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v2
+        with:
+          username: ${{ secrets.DOCKER_HUB_USERNAME }} 
+          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+      # Log in to GitHub Container Registry (GHCR)
+      - name: Log in to GHCR
+        uses: docker/login-action@v2
+        with:
+          registry: ghcr.io
+          username: ${{ github.actor }}
+          password: ${{ secrets.GITHUB_TOKEN }}
+
+      # Determine which directories have changes
+      - name: Check for Changes
+        id: changes
+        run: |
+          echo "## Detecting changes in the repository..."
+          if git diff --name-only HEAD^ HEAD | grep -q 'session_ml/DeepLearningDataIntegration'; then
+            echo "deep_learning=true" >> $GITHUB_ENV
+          fi
+          if git diff --name-only HEAD^ HEAD | grep -q 'session_ml/FeatureSelectionIntegrOMICs'; then
+            echo "feature_selection=true" >> $GITHUB_ENV
+          fi
+          if git diff --name-only HEAD^ HEAD | grep -q 'session_ml/SingleCell'; then
+            echo "single_cell=true" >> $GITHUB_ENV
+          fi
+          if git diff --name-only HEAD^ HEAD | grep -q 'session_gems'; then
+            echo "gems=true" >> $GITHUB_ENV
+          fi
+
+      # Conditionally build and push images for Deep Learning Lab
+      - name: Build and Push Docker Image for Deep Learning Lab
+        if: env.deep_learning == 'true'
+        uses: docker/build-push-action@v4
+        with:
+          context: ./session_ml/DeepLearningDataIntegration
+          file: session_ml/DeepLearningDataIntegration/Dockerfile
+          platforms: linux/amd64
+          push: true
+          no-cache: true
+          tags: |
+            docker.io/rasoolsnbis/omicsint_h24:session_ml_deep_learning_integration_amd
+            ghcr.io/nbisweden/omicsint_h24:session_ml_deep_learning_integration_amd
+
+      # Conditionally build and push images for Feature Selection Lab
+      - name: Build and Push Docker Image for Feature Selection Lab
+        if: env.feature_selection == 'true'
+        uses: docker/build-push-action@v4
+        with:
+          context: ./session_ml/FeatureSelectionIntegrOMICs
+          file: session_ml/FeatureSelectionIntegrOMICs/Dockerfile
+          platforms: linux/amd64
+          push: true
+          no-cache: true
+          tags: |
+            docker.io/rasoolsnbis/omicsint_h24:session_ml_feature_selection_amd
+            ghcr.io/nbisweden/omicsint_h24:session_ml_feature_selection_amd
+
+      # Conditionally build and push images for Single Cell Lab
+      - name: Build and Push Docker Image for Single Cell Lab
+        if: env.single_cell == 'true'
+        uses: docker/build-push-action@v4
+        with:
+          context: ./session_ml/SingleCell
+          file: session_ml/SingleCell/Dockerfile
+          platforms: linux/amd64
+          push: true
+          no-cache: true
+          tags: |
+            docker.io/rasoolsnbis/omicsint_h24:session_ml_single_cell_amd
+            ghcr.io/nbisweden/omicsint_h24:session_ml_single_cell_amd
+
+      # Conditionally build and push images for Gems Lab
+      - name: Build and Push Docker Image for Gems Lab
+        if: env.gems == 'true'
+        uses: docker/build-push-action@v4
+        with:
+          context: ./session_gems
+          file: session_gems/Dockerfile
+          platforms: linux/amd64
+          push: true
+          no-cache: true
+          tags: |
+            docker.io/rasoolsnbis/omicsint_h24:session_gems_amd
+            ghcr.io/nbisweden/omicsint_h24:session_gems_amd

.github/workflows/docker-build-lab-Single_cell-amd.yml

@@ -1,63 +1,44 @@
-name: Build and Push Docker Image for lab single cell 
-
-on:
-  push:
-    paths:
-      - 'session_ml/SingleCell/**'
-    branches:
-      - OMICSINT_H24
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-
-    if: github.repository == 'nbisweden/workshop_omics_integration'
-
-    steps:
-      # Checkout the repository
-      - name: Checkout repository
-        uses: actions/checkout@v3
-
-      # Set up Docker Buildx for multi-platform builds
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-
-      # Log in to Docker Hub using the secrets
-      - name: Log in to Docker Hub
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKER_HUB_USERNAME }} 
-          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
-
-      # Log in to GitHub Container Registry (GHCR)
-      - name: Log in to GHCR
-        uses: docker/login-action@v2
-        with:
-          registry: ghcr.io
-          username: ${{ github.actor }}
-          password: ${{ secrets.GITHUB_TOKEN }}
-
-      # Build and push the Docker image for both amd64 to Docker Hub
-      - name: Build and Push Docker Image to Docker Hub
-        uses: docker/build-push-action@v4
-        with:
-          context: ./session_ml/SingleCell
-          file: session_ml/SingleCell/Dockerfile
-          platforms: linux/amd64
-          push: true
-          no-cache: true
-          tags: docker.io/rasoolsnbis/omicsint_h24:session_ml_single_cell_amd
-
-      # Build and push the Docker image to GitHub Container Registry (GHCR)
-      - name: Build and Push Docker Image to GHCR
-        uses: docker/build-push-action@v4
-        with:
-          context: ./session_ml/SingleCell
-          file: session_ml/SingleCell/Dockerfile
-          platforms: linux/amd64
-          push: true
-          no-cache: true
-          tags: ghcr.io/nbisweden/omicsint_h24:session_ml_single_cell_amd
-
-      - name: Inspect Docker Image
-        run: docker buildx imagetools inspect docker.io/rasoolsnbis/omicsint_h24:session_ml_single_cell_amd
+# name: Build and Push Docker Image for lab single cell 
+
+# on:
+#   push:
+#     paths:
+#       - 'session_ml/SingleCell/**'
+#     branches:
+#       - OMICSINT_H24
+
+# jobs:
+#   build:
+#     runs-on: ubuntu-latest
+
+#     if: github.repository == 'nbisweden/workshop_omics_integration'
+
+#     steps:
+#       # Checkout the repository
+#       - name: Checkout repository
+#         uses: actions/checkout@v3
+
+#       # Set up Docker Buildx for multi-platform builds
+#       - name: Set up Docker Buildx
+#         uses: docker/setup-buildx-action@v2
+
+#       # Log in to Docker Hub using the secrets
+#       - name: Log in to Docker Hub
+#         uses: docker/login-action@v2
+#         with:
+#           username: ${{ secrets.DOCKER_HUB_USERNAME }} 
+#           password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+#       # Build and push the Docker image for both amd64 to Docker Hub
+#       - name: Build and Push Docker Image to Docker Hub
+#         uses: docker/build-push-action@v4
+#         with:
+#           context: ./session_ml/SingleCell
+#           file: session_ml/SingleCell/Dockerfile
+#           platforms: linux/amd64
+#           push: true
+#           no-cache: true
+#           tags: docker.io/rasoolsnbis/omicsint_h24:session_ml_single_cell_amd
+
+#       - name: Inspect Docker Image
+#         run: docker buildx imagetools inspect docker.io/rasoolsnbis/omicsint_h24:session_ml_single_cell_amd

.github/workflows/docker-build-lab-deep-learning-integration-amd.yml

@@ -1,44 +1,44 @@
-name: Build and Push Docker Image for lab deep learning integration 
-
-on:
-  push:
-    paths:
-      - 'session_ml/DeepLearningDataIntegration/**'
-    branches:
-      - OMICSINT_H24
-
-jobs:
-  build:
-    runs-on: ubuntu-latest
-
-    if: github.repository == 'NBISweden/workshop_omics_integration'
-
-    steps:
-      # Checkout the repository
-      - name: Checkout repository
-        uses: actions/checkout@v3
-
-      # Set up Docker Buildx for multi-platform builds
-      - name: Set up Docker Buildx
-        uses: docker/setup-buildx-action@v2
-
-      # Log in to Docker Hub using the secrets
-      - name: Log in to Docker Hub
-        uses: docker/login-action@v2
-        with:
-          username: ${{ secrets.DOCKER_HUB_USERNAME }} 
-          password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
-
-      # Build and push the Docker image for both amd64 and arm64
-      - name: Build and Push Docker Image for Session Gems
-        uses: docker/build-push-action@v4
-        with:
-          context: ./session_ml/DeepLearningDataIntegration
-          file: session_ml/DeepLearningDataIntegration/Dockerfile
-          platforms: linux/amd64
-          push: true
-          no-cache: true
-          tags: docker.io/rasoolsnbis/omicsint_h24:session_ml_deep_learning_integration_amd
-
-      - name: Inspect Docker Image
-        run: docker buildx imagetools inspect docker.io/rasoolsnbis/omicsint_h24:session_ml_deep_learning_integration_amd
+# name: Build and Push Docker Image for lab deep learning integration 
+
+# on:
+#   push:
+#     paths:
+#       - 'session_ml/DeepLearningDataIntegration/**'
+#     branches:
+#       - OMICSINT_H24
+
+# jobs:
+#   build:
+#     runs-on: ubuntu-latest
+
+#     if: github.repository == 'NBISweden/workshop_omics_integration'
+
+#     steps:
+#       # Checkout the repository
+#       - name: Checkout repository
+#         uses: actions/checkout@v3
+
+#       # Set up Docker Buildx for multi-platform builds
+#       - name: Set up Docker Buildx
+#         uses: docker/setup-buildx-action@v2
+
+#       # Log in to Docker Hub using the secrets
+#       - name: Log in to Docker Hub
+#         uses: docker/login-action@v2
+#         with:
+#           username: ${{ secrets.DOCKER_HUB_USERNAME }} 
+#           password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+#       # Build and push the Docker image for both amd64 and arm64
+#       - name: Build and Push Docker Image for Session Gems
+#         uses: docker/build-push-action@v4
+#         with:
+#           context: ./session_ml/DeepLearningDataIntegration
+#           file: session_ml/DeepLearningDataIntegration/Dockerfile
+#           platforms: linux/amd64
+#           push: true
+#           no-cache: true
+#           tags: docker.io/rasoolsnbis/omicsint_h24:session_ml_deep_learning_integration_amd
+
+#       - name: Inspect Docker Image
+#         run: docker buildx imagetools inspect docker.io/rasoolsnbis/omicsint_h24:session_ml_deep_learning_integration_amd

.github/workflows/docker-build-lab-feature-selection-amd.yml

@@ -0,0 +1,44 @@
+# name: Build and Push Docker Image for lab feature selection 
+
+# on:
+#   push:
+#     paths:
+#       - 'session_ml/FeatureSelectionIntegrOMICs/**'
+#     branches:
+#       - OMICSINT_H24
+
+# jobs:
+#   build:
+#     runs-on: ubuntu-latest
+
+#     if: github.repository == 'nbisweden/workshop_omics_integration'
+
+#     steps:
+#       # Checkout the repository
+#       - name: Checkout repository
+#         uses: actions/checkout@v3
+
+#       # Set up Docker Buildx for multi-platform builds
+#       - name: Set up Docker Buildx
+#         uses: docker/setup-buildx-action@v2
+
+#       # Log in to Docker Hub using the secrets
+#       - name: Log in to Docker Hub
+#         uses: docker/login-action@v2
+#         with:
+#           username: ${{ secrets.DOCKER_HUB_USERNAME }} 
+#           password: ${{ secrets.DOCKER_HUB_ACCESS_TOKEN }}
+
+#       # Build and push the Docker image for both amd64 to Docker Hub
+#       - name: Build and Push Docker Image to Docker Hub
+#         uses: docker/build-push-action@v4
+#         with:
+#           context: ./session_ml/FeatureSelectionIntegrOMICs
+#           file: session_ml/FeatureSelectionIntegrOMICs/Dockerfile
+#           platforms: linux/amd64
+#           push: true
+#           no-cache: true
+#           tags: docker.io/rasoolsnbis/omicsint_h24:session_ml_feature_selection_amd
+
+#       - name: Inspect Docker Image
+#         run: docker buildx imagetools inspect docker.io/rasoolsnbis/omicsint_h24:session_ml_feature_selection_amd