Configure PRODIGY pipeline for WES execution with S3 and Harbor

Dockerfile

@@ -0,0 +1,40 @@
+FROM python:3.12
+
+LABEL maintainer="Omic"
+LABEL description="PRODIGY - PROtein binDIng enerGY prediction"
+LABEL version="2.4.0"
+
+# Set environment variables
+ENV DEBIAN_FRONTEND=noninteractive
+ENV PYTHONUNBUFFERED=1
+
+# Install system dependencies required for freesasa compilation
+RUN apt-get update -y && \
+    apt-get install -y --no-install-recommends \
+    build-essential \
+    gcc \
+    g++ \
+    make \
+    procps \
+    && rm -rf /var/lib/apt/lists/*
+
+# Upgrade pip
+RUN pip install --no-cache-dir --upgrade pip
+
+# Install PRODIGY and its dependencies
+# Dependencies: biopython>=1.80, freesasa>=2.2.1, numpy>=2
+RUN pip install --no-cache-dir \
+    "biopython>=1.80" \
+    "freesasa>=2.2.1" \
+    "numpy>=2"
+
+# Install PRODIGY
+RUN pip install --no-cache-dir prodigy-prot==2.4.0
+
+# Verify installation
+RUN prodigy --help
+
+# Set working directory
+WORKDIR /data
+
+CMD ["prodigy", "--help"]