Merge pull request #106 from rasools/OMICSINT_H24

Add session_ml_deep_learning_integration_amd workflow

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

@@ -1,9 +1,9 @@
-name: Build and Push Docker Image for Session Gems
+name: Build and Push Docker Image for lab deep learning integration 
 
 on:
   push:
     paths:
-      - 'session_gems/**'
+      - 'session_ml/DeepLearningDataIntegration/**'
     branches:
       - OMICSINT_H24
 
@@ -34,10 +34,10 @@ jobs:
         uses: docker/build-push-action@v4
         with:
           context: ./session_gems
-          file: session_gems/Dockerfile
-          platforms: linux/arm64
+          file: session_ml/DeepLearningDataIntegration/Dockerfile
+          platforms: linux/amd64
           push: true
-          tags: docker.io/rasoolsnbis/omicsint_h24:session_gems_arm
+          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_gems_arm
+        run: docker buildx imagetools inspect docker.io/rasoolsnbis/omicsint_h24:session_ml_deep_learning_integration_amd

session_ml/DeepLearningDataIntegration/Dockerfile

@@ -14,6 +14,13 @@ USER root
 RUN apt-get update && apt-get install curl -y --no-install-recommends && \
     apt-get clean && rm -rf /var/lib/apt/lists/*
 
+# Clone the data folder from GitHub
+RUN git clone --depth=1 --filter=blob:none --sparse https://github.com/NBISweden/workshop_omics_integration.git /tmp/repo && \
+    cd /tmp/repo && \
+    git sparse-checkout set session_gems/lab/data && \
+    mv session_ml/DeepLearningDataIntegration/lab/data /home/jovyan/lab/data && \
+    rm -rf /tmp/repo
+
 # Install pip requirements as root
 RUN pip install --no-cache-dir -r /tmp/requirements.txt