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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/
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