--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Dockerfile	Fri Sep 11 21:58:43 2026 +0000
@@ -0,0 +1,91 @@
+# =============================================================
+#   Dockerfile for mitokmer2 (compatible with Galaxy/AWS Batch)
+# =============================================================
+
+# ---------- Build Stage ----------
+FROM ubuntu:focal AS build
+
+ARG DEBIAN_FRONTEND=noninteractive
+ARG PYTHON_VER="3.8"
+
+WORKDIR /workspace
+
+# Build dependencies: compiler, zlib dev headers, git, Python
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    build-essential \
+    g++ \
+    git \
+    wget \
+    zlib1g-dev \
+    ca-certificates \
+    python${PYTHON_VER} \
+    python${PYTHON_VER}-dev \
+    python${PYTHON_VER}-venv \
+    && rm -rf /var/lib/apt/lists/*
+
+# Create Python virtual environment using --copies so symlinks
+# do not break when the venv is copied to the runtime stage
+RUN python${PYTHON_VER} -m venv --copies /opt/venv
+ENV PATH="/opt/venv/bin:${PATH}"
+
+# Install Python dependencies
+RUN pip install --no-cache-dir -U pip && \
+    pip install --no-cache-dir pandas
+
+# Clone mitokmer2 source code from GitHub
+RUN git clone https://github.com/mmammel8/mitokmer2.git /opt/mitokmer2
+
+WORKDIR /opt/mitokmer2
+
+# Compile the C++ read-screening program
+# kmer_read_1.cpp -> kmerread
+RUN g++ -O3 kmer_read_1.cpp -o kmerread -lz && \
+    chmod +x kmerread
+
+# Install any Python requirements declared in the repo
+RUN if [ -f requirements.txt ]; then \
+        pip install --no-cache-dir -r requirements.txt; \
+    fi
+
+
+# ---------- Runtime Stage ----------
+FROM ubuntu:focal AS runtime
+
+ARG DEBIAN_FRONTEND=noninteractive
+
+# Lean runtime: zlib shared library + Python runtime only
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    zlib1g \
+    libbz2-1.0 \
+    ca-certificates \
+    python3.8 \
+    python3.8-venv \
+    python3.8-distutils \
+    && rm -rf /var/lib/apt/lists/*
+
+# Copy compiled binary from build stage
+COPY --from=build /opt/mitokmer2/kmerread /usr/local/bin/kmerread
+
+# Copy Python scripts and supporting files from build stage
+COPY --from=build /opt/mitokmer2 /opt/mitokmer2
+
+# Copy Python virtual environment from build stage
+# --copies in the build stage ensures no broken symlinks here
+COPY --from=build /opt/venv /opt/venv
+
+# Refresh the dynamic linker cache so zlib and other shared
+# libraries are found at runtime
+RUN ldconfig || true
+
+# Ensure all users (including arbitrary Galaxy UIDs) can
+# read and execute binaries, scripts, and the venv
+RUN chmod a+rx  /usr/local/bin/kmerread && \
+    chmod -R a+rX /opt/mitokmer2 && \
+    chmod -R a+rX /opt/venv
+
+# Runtime environment
+ENV PATH="/opt/venv/bin:/opt/mitokmer2:/usr/local/bin:${PATH}" \
+    LC_ALL=C
+
+# IMPORTANT: No ENTRYPOINT for Galaxy/AWS Batch. Neutral CMD.
+CMD ["/bin/bash"]