Singularity Container

.ipynb_checkpoints/Singularity-checkpoint

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+Bootstrap: docker
+From: python:3.8-slim-buster
+
+%setup
+    # Commands to set up the build environment, if necessary
+    mkdir -p /app
+
+%post
+    # Set the working directory
+    cd /app
+
+    # Install system dependencies
+    apt-get update && \
+    apt-get install -y build-essential openslide-tools libgl1-mesa-glx && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+    # Copy the application code
+    cp -r $SINGULARITY_BUILDDEF_DIR/* /app/
+
+    # Install Python dependencies
+    pip install -r /app/requirements.txt
+
+    # Create a non-root user (similar to the Docker ARG approach)
+    useradd -m -s /bin/bash -u ${USER_ID:-1000} myuser
+
+%environment
+    # Set environment variables, if needed
+    export HOME=/home/myuser
+    export PATH=/app:$PATH
+
+%runscript
+    # Script that is executed when the container is run
+    exec /bin/bash
+
+%labels
+    Author Vatsal_Patel
+    Version version2
+
+%files
+    # Files to copy from the current directory into the container
+    ./ /app/

Singularity

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+Bootstrap: docker
+From: python:3.8-slim-buster
+
+%setup
+    # Commands to set up the build environment, if necessary
+    mkdir -p /app
+
+%post
+    # Set the working directory
+    cd /app
+
+    # Install system dependencies
+    apt-get update && \
+    apt-get install -y build-essential openslide-tools libgl1-mesa-glx && \
+    apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+    # Copy the application code
+    cp -r $SINGULARITY_BUILDDEF_DIR/* /app/
+
+    # Install Python dependencies
+    pip install -r /app/requirements.txt
+
+    # Create a non-root user (similar to the Docker ARG approach)
+    useradd -m -s /bin/bash -u ${USER_ID:-1000} myuser
+
+%environment
+    # Set environment variables, if needed
+    export HOME=/home/myuser
+    export PATH=/app:$PATH
+
+%runscript
+    # Script that is executed when the container is run
+    exec /bin/bash
+
+%labels
+    Author Vatsal_Patel
+    Version version2
+
+%files
+    # Files to copy from the current directory into the container
+    ./ /app/