diff --git a/.github/workflows/docker-build-lab-gems-arm.yml b/.github/workflows/docker-build-lab-deep-learning-integration-amd.yml similarity index 73% rename from .github/workflows/docker-build-lab-gems-arm.yml rename to .github/workflows/docker-build-lab-deep-learning-integration-amd.yml index 91e7213..7022c6e 100644 --- a/.github/workflows/docker-build-lab-gems-arm.yml +++ b/.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 diff --git a/session_ml/DeepLearningDataIntegration/Dockerfile b/session_ml/DeepLearningDataIntegration/Dockerfile index fa5109e..04e8721 100644 --- a/session_ml/DeepLearningDataIntegration/Dockerfile +++ b/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