Restore Docker image to build process

broadinstitute · Oct 15, 2024 · b006d1a · b006d1a
1 parent 89785a1
commit b006d1a
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Showing 2 changed files with 53 additions and 49 deletions.
diff --git a/.github/workflows/cd.yml b/.github/workflows/cd.yml
@@ -73,37 +73,37 @@ jobs:
         asset_name: hidive-${{ steps.version-bump.outputs.new_ver }}
         asset_content_type: application/octet-stream
 
-    # - name: Authenticate to Google Cloud
-    #   id: 'auth'
-    #   uses: 'google-github-actions/auth@v1'
-    #   with:
-    #     credentials_json: '${{ secrets.GOOGLE_CREDENTIALS }}'
+    - name: Authenticate to Google Cloud
+      id: 'auth'
+      uses: 'google-github-actions/auth@v1'
+      with:
+        credentials_json: '${{ secrets.GOOGLE_CREDENTIALS }}'
 
-    # - name: Set up Docker Buildx
-    #   uses: docker/setup-buildx-action@v2
+    - name: Set up Docker Buildx
+      uses: docker/setup-buildx-action@v2
 
-    # - name: Cache Docker layers
-    #   uses: actions/cache@v3
-    #   with:
-    #     path: /tmp/.buildx-cache
-    #     key: ${{ runner.os }}-buildx-${{ github.sha }}
-    #     restore-keys: |
-    #       ${{ runner.os }}-buildx-
+    - name: Cache Docker layers
+      uses: actions/cache@v3
+      with:
+        path: /tmp/.buildx-cache
+        key: ${{ runner.os }}-buildx-${{ github.sha }}
+        restore-keys: |
+          ${{ runner.os }}-buildx-
 
-    # - name: Configure Docker to use gcloud credentials
-    #   run: gcloud auth configure-docker us.gcr.io -q
+    - name: Configure Docker to use gcloud credentials
+      run: gcloud auth configure-docker us.gcr.io -q
 
-    # - name: Build and push Docker image
-    #   uses: docker/build-push-action@v4
-    #   with:
-    #     context: ./docker
-    #     push: true
-    #     tags: us.gcr.io/broad-dsp-lrma/lr-hidive:${{ steps.version-bump.outputs.new_ver }}
-    #     build-args: |
-    #       branch=v${{ steps.version-bump.outputs.new_ver }}
-    #     cache-from: |
-    #       type=local,src=/tmp/.buildx-cache
-    #       type=gha,scope=${{ github.workflow }}
-    #     cache-to: |
-    #       type=local,dest=/tmp/.buildx-cache-new,mode=max
-    #       type=gha,mode=max,scope=${{ github.workflow }}
+    - name: Build and push Docker image
+      uses: docker/build-push-action@v4
+      with:
+        context: ./docker
+        push: true
+        tags: us.gcr.io/broad-dsp-lrma/lr-hidive:${{ steps.version-bump.outputs.new_ver }}
+        build-args: |
+          branch=v${{ steps.version-bump.outputs.new_ver }}
+        cache-from: |
+          type=local,src=/tmp/.buildx-cache
+          type=gha,scope=${{ github.workflow }}
+        cache-to: |
+          type=local,dest=/tmp/.buildx-cache-new,mode=max
+          type=gha,mode=max,scope=${{ github.workflow }}
diff --git a/docker/Dockerfile b/docker/Dockerfile
@@ -38,23 +38,23 @@ RUN pip3 uninstall -y crcmod && \
 # Fix python malloc bug
 RUN echo 'export LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libtcmalloc_minimal.so.4"' >> ~/.bashrc
 
-# Create known hosts for github ssh info
-RUN mkdir -p ~/.ssh && \
-    touch ~/.ssh/known_hosts && \
-    ssh-keyscan github.com >> ~/.ssh/known_hosts
-
-# Install cargo
-RUN curl https://sh.rustup.rs -sSf | sh -s -- -y
-ENV PATH="/root/.cargo/bin:${PATH}"
-
-# Install hidive
-RUN git clone https://github.com/broadinstitute/hidive.git && \
-    cd hidive && \
-    git checkout $branch && \
-    cargo build --release && \
-    cp target/release/hidive /usr/local/bin/ && \
-    cd .. && \
-    rm -rf hidive
+# # Create known hosts for github ssh info
+# RUN mkdir -p ~/.ssh && \
+#     touch ~/.ssh/known_hosts && \
+#     ssh-keyscan github.com >> ~/.ssh/known_hosts
+
+# # Install cargo
+# RUN curl https://sh.rustup.rs -sSf | sh -s -- -y
+# ENV PATH="/root/.cargo/bin:${PATH}"
+
+# # Install hidive
+# RUN git clone https://github.com/broadinstitute/hidive.git && \
+#     cd hidive && \
+#     git checkout $branch && \
+#     cargo build --release && \
+#     cp target/release/hidive /usr/local/bin/ && \
+#     cd .. && \
+#     rm -rf hidive
 
 # Install minimap2
 RUN wget -O minimap2-2.28.tar.bz2 https://github.com/lh3/minimap2/releases/download/v2.28/minimap2-2.28.tar.bz2 && \
@@ -78,7 +78,8 @@ RUN wget -O samtools-1.21.tar.bz2 https://github.com/samtools/samtools/releases/
 FROM python:3.9-slim
 
 # Copy necessary files from builder stage
-COPY --from=builder /usr/local/bin/hidive /usr/local/bin/hidive
+#COPY --from=builder /usr/local/bin/hidive /usr/local/bin/hidive
+
 COPY --from=builder /usr/local/bin/minimap2 /usr/local/bin/minimap2
 COPY --from=builder /usr/local/bin/samtools /usr/local/bin/samtools
 COPY --from=builder /usr/lib/x86_64-linux-gnu/libtcmalloc_minimal.so.4 /usr/lib/x86_64-linux-gnu/libtcmalloc_minimal.so.4
@@ -91,4 +92,7 @@ ENV PATH="/root/.cargo/bin:/google-cloud-sdk/bin:${PATH}"
 ENV LD_PRELOAD="/usr/lib/x86_64-linux-gnu/libtcmalloc_minimal.so.4"
 
 # We want this to be interactive
-CMD ["/bin/bash"]
+CMD ["/bin/bash"]
+
+# Copy hidive binary from Github action artifact
+COPY ./target/release/hidive /usr/local/bin/hidive