--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Dockerfile	Mon Mar 16 15:02:07 2026 +0000
@@ -0,0 +1,74 @@
+# =============================================================
+#   Dockerfile for refchooser (compatible with Galaxy)
+# =============================================================
+
+# ---------- Build Stage 1: The "Builder" ----------
+# This stage downloads and prepares all our dependencies.
+FROM ubuntu:20.04 AS builder
+
+# Set versions for our tools to make updates easy.
+ARG MASH_VER="2.3"
+ARG PYTHON_VER="3.8"
+
+# Avoid interactive prompts during apt-get install.
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install all the dependencies needed to build our tools.
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    wget \
+    tar \
+    gzip \
+    python${PYTHON_VER} \
+    python${PYTHON_VER}-venv \
+    && rm -rf /var/lib/apt/lists/*
+
+# Set a working directory for our downloads.
+WORKDIR /build
+
+# --- Install Mash ---
+# Download the pre-compiled Linux binary for Mash.
+ADD https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar .
+# Unpack the tarball, find the 'mash' executable, and install it to a standard location.
+RUN tar -xvf mash-Linux64-v${MASH_VER}.tar && \
+    install -m 0755 mash-Linux64-v${MASH_VER}/mash /usr/local/bin/mash
+
+# --- Install refchooser ---
+# Create a Python virtual environment in a standard location.
+RUN python${PYTHON_VER} -m venv /opt/venv
+# Activate the venv and install refchooser and its dependencies using pip.
+ENV PATH="/opt/venv/bin:$PATH"
+RUN pip install --no-cache-dir refchooser
+
+
+# ---------- Build Stage 2: The "Runtime" Stage ----------
+# This is our final, lean image that will be used by Galaxy.
+FROM ubuntu:20.04 AS runtime
+
+# Avoid interactive prompts.
+ENV DEBIAN_FRONTEND=noninteractive
+
+# Install only the essential runtime libraries needed by Mash and Python.
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    libgomp1 \
+    python3.8-venv \
+    && rm -rf /var/lib/apt/lists/*
+
+# --- Copy Binaries and Environment from Builder Stage ---
+
+# Copy the compiled 'mash' binary from the builder stage.
+COPY --from=builder /usr/local/bin/mash /usr/local/bin/mash
+
+# Copy the entire Python virtual environment containing 'refchooser'.
+COPY --from=builder /opt/venv /opt/venv
+
+# --- Final Configuration ---
+
+# Set the PATH environment variable so the system can find 'mash' and 'refchooser'.
+ENV PATH="/opt/venv/bin:$PATH"
+
+# As a best practice for Galaxy, ensure all users can read and execute the tools.
+RUN chmod -R a+rX /opt/venv && \
+    chmod a+rx /usr/local/bin/mash
+
+# IMPORTANT: No ENTRYPOINT. Set a neutral CMD for Galaxy compatibility.
+CMD ["/bin/bash"]