Dev

.github/workflows/build_deploy_container.yaml

@@ -29,7 +29,7 @@ jobs:
     steps:
     - name: Checkout code
       uses: actions/checkout@v2
-
+      
     - name: Export Secrets to Environment
       run: |
         echo "SINGULARITY_LIBRARY_TOKEN=${{ secrets.SINGULARITY_LIBRARY_TOKEN }}" >> $GITHUB_ENV
@@ -53,30 +53,29 @@ jobs:
       run: |
         docker buildx build --platform linux/amd64 -f $DOCKERFILE_PATH -t $DOCKER_IMAGE_NAME:latest -t $DOCKER_IMAGE_NAME:${{ steps.set_tag.outputs.tag }} --push .
 
-    - name: Clean up Docker build artifacts
-      run: |
-        docker system prune -af
-
+    - name: Maximize build disk space
+      uses: easimon/maximize-build-space@v10
+      with:
+        root-reserve-mb: 512
+        swap-size-mb: 1024
+        remove-dotnet: 'true'
+
     - name: Setup Apptainer
       uses: eWaterCycle/setup-apptainer@v2.0.0
 
     - name: Configure Singularity temp directories
       run: |
-        # create a temp area inside the GitHub runner's large temp folder
-        mkdir -p $RUNNER_TEMP/singularity
-        echo "APPTAINER_TMPDIR=$RUNNER_TEMP/singularity" >> $GITHUB_ENV
-        # optional: keep a separate cache dir
-        mkdir -p $RUNNER_TEMP/singularity/cache
-        echo "APPTAINER_CACHEDIR=$RUNNER_TEMP/singularity/cache" >> $GITHUB_ENV
-
-    - name: Check free space
-      run: |
-        df -h
-
+        mkdir -p "$GITHUB_WORKSPACE/.singularity/cache"
+        echo "APPTAINER_TMPDIR=$GITHUB_WORKSPACE/.singularity" >> $GITHUB_ENV
+        echo "APPTAINER_CACHEDIR=$GITHUB_WORKSPACE/.singularity/cache" >> $GITHUB_ENV
+
     - name: Convert Docker Image to Singularity SIF
       run: |
-        apptainer pull --disable-cache --tmpdir $RUNNER_TEMP/singularity /mnt/genopred_image.sif docker://${DOCKER_IMAGE_NAME}:latest
-
+        apptainer pull --disable-cache \
+          --tmpdir "$GITHUB_WORKSPACE/.singularity" \
+          "$GITHUB_WORKSPACE/genopred_image.sif" \
+          docker://${DOCKER_IMAGE_NAME}:latest
+
     - name: Install expect
       run: |
         sudo apt-get update
@@ -98,14 +97,17 @@ jobs:
         send -- "${{ secrets.SIGNING_KEY_PASSWORD }}\r"
         expect eof
         '
+
     - name: Sign the Singularity Image
       run: |
-        expect -c '
-        spawn apptainer sign /mnt/genopred_image.sif
-        expect "Enter your key passphrase : "
-        send -- "${{ secrets.SIGNING_KEY_PASSWORD }}\r"
-        expect eof
-        '
+        SIF_PATH="$GITHUB_WORKSPACE/genopred_image.sif"
+        expect -c "
+          spawn apptainer sign \"$SIF_PATH\"
+          expect \"Enter your key passphrase : \"
+          send -- \"${{ secrets.SIGNING_KEY_PASSWORD }}\r\"
+          expect eof
+        "
+
     - name: Create Token File
       run: echo "${{ secrets.SINGULARITY_LIBRARY_TOKEN }}" > tokenfile
 
@@ -117,7 +119,7 @@ jobs:
 
     - name: Push Singularity Image to Singularity Library
       run: |
-        apptainer push /mnt/genopred_image.sif $SINGULARITY_IMAGE_NAME:latest
+        apptainer push "$GITHUB_WORKSPACE/genopred_image.sif" "$SINGULARITY_IMAGE_NAME:latest"
 
     - name: Setup tmate session
       if: ${{ failure() }}

pipeline/misc/docker/Dockerfile

@@ -10,10 +10,10 @@ RUN apt-get update && \
     echo 'exec /bin/tar --no-same-owner "$@"' >> /usr/local/bin/tar && \
     chmod +x /usr/local/bin/tar
 
-# Install Mambaforge
-RUN wget https://github.com/conda-forge/miniforge/releases/download/4.10.3-10/Mambaforge-4.10.3-10-Linux-x86_64.sh && \
-    bash Mambaforge-4.10.3-10-Linux-x86_64.sh -b -p /opt/mambaforge && \
-    rm Mambaforge-4.10.3-10-Linux-x86_64.sh
+# Install Miniforge
+RUN wget https://github.com/conda-forge/miniforge/releases/download/24.11.3-0/Miniforge3-24.11.3-0-Linux-x86_64.sh && \
+    bash Miniforge3-24.11.3-0-Linux-x86_64.sh -b -p /opt/miniforge && \
+    rm Miniforge3-24.11.3-0-Linux-x86_64.sh
 
 # Download GenoPred
 RUN mkdir -p /tools/GenoPred && \
@@ -22,20 +22,20 @@ RUN mkdir -p /tools/GenoPred && \
     git fetch --tags
 
 # Create genopred env
-RUN /opt/mambaforge/bin/conda init bash && \
-    echo "source /opt/mambaforge/etc/profile.d/conda.sh" >> /etc/bash.bashrc && \
-    . /opt/mambaforge/etc/profile.d/conda.sh && \
+RUN /opt/miniforge/bin/conda init bash && \
+    echo "source /opt/miniforge/etc/profile.d/conda.sh" >> /etc/bash.bashrc && \
+    . /opt/miniforge/etc/profile.d/conda.sh && \
     mamba env update -n genopred -f /tools/GenoPred/pipeline/envs/pipeline.yaml && \
     mamba clean -a -y
 
 # Run initial snakemake command to setup dependencies
-RUN /opt/mambaforge/bin/conda init bash && \
-    echo "source /opt/mambaforge/etc/profile.d/conda.sh" >> /etc/bash.bashrc && \
-    . /opt/mambaforge/etc/profile.d/conda.sh && \
+RUN /opt/miniforge/bin/conda init bash && \
+    echo "source /opt/miniforge/etc/profile.d/conda.sh" >> /etc/bash.bashrc && \
+    . /opt/miniforge/etc/profile.d/conda.sh && \
     conda activate genopred && \
     cd /tools/GenoPred/pipeline && \
     snakemake --restart-times 3 -j1 --use-conda --conda-frontend mamba install_r_packages resources/software/pgscatalog_utils/download_pgscatalog_utils.done && \
     mamba clean -a -y
 
 ENTRYPOINT ["/bin/bash"]
-CMD ["-c", "source /opt/mambaforge/etc/profile.d/conda.sh && conda init && source ~/.bashrc && conda activate genopred && cd /tools/GenoPred/pipeline && exec /bin/bash"]
+CMD ["-c", "source /opt/miniforge/etc/profile.d/conda.sh && conda init && source ~/.bashrc && conda activate genopred && cd /tools/GenoPred/pipeline && exec /bin/bash"]