--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Dockerfile	Fri May 15 11:44:48 2026 +0000
@@ -0,0 +1,137 @@
+# Multi-stage Dockerfile for SeqSero2S
+# Default build: docker build -t seqsero2s:latest .
+# Test build: docker build --target test -t seqsero2s:test .
+
+# ============================================================================
+# Stage 1: Base image with mambaforge for faster dependency resolution
+# ============================================================================
+FROM condaforge/mambaforge:latest AS base
+
+LABEL maintainer="SeqSero2S Maintainers"
+LABEL description="Simplified Salmonella serotype prediction from genome sequencing data"
+
+# Set environment variables to reduce conda output and ensure non-interactive
+# Disable SSL verification for VPN environments
+ENV CONDA_ALWAYS_YES=true \
+    CONDA_AUTO_UPDATE_CONDA=false \
+    DEBIAN_FRONTEND=noninteractive
+
+# Configure conda to skip SSL verification
+RUN conda config --set ssl_verify false
+
+# ============================================================================
+# Stage 2: Builder - Install all dependencies and SeqSero2S
+# ============================================================================
+FROM base AS builder
+
+# Update base packages and install build essentials
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        wget \
+        ca-certificates \
+        bash \
+    && apt-get clean && \
+    rm -rf /var/lib/apt/lists/*
+
+# Copy the patch script
+COPY patch_stringmlst.sh /tmp/patch_stringmlst.sh
+RUN chmod +x /tmp/patch_stringmlst.sh
+
+# Create conda environment with all dependencies
+# Using mamba for faster dependency resolution
+RUN mamba create -n seqsero2s -c conda-forge -c bioconda \
+    python>=3 \
+    pip \
+    setuptools \
+    blast>=2.2 \
+    zstd \
+    samtools \
+    bedtools>=2.17 \
+    sra-tools>=2.8 \
+    spades>=3.9 \
+    salmid \
+    bwa>=0.7 \
+    seqtk>=1.3 \
+    stringmlst>=0.6 \
+    mlst>=2.32.2 \
+    perl-list-moreutils \
+    && mamba clean -afy
+
+# Install SeqSero2S from local fork
+WORKDIR /tmp/build
+
+# Copy local SeqSero2S directory
+COPY SeqSero2S /tmp/build/SeqSero2S
+
+# Install SeqSero2S
+RUN cd SeqSero2S && \
+    /opt/conda/envs/seqsero2s/bin/python -m pip install . -vv --no-deps --no-build-isolation --no-cache-dir
+
+# Apply the stringMLST.py patch (from the conda recipe)
+# The patch replaces dbPrefix reference with cwd to avoid path issues
+RUN PREFIX=/opt/conda/envs/seqsero2s /tmp/patch_stringmlst.sh
+
+# ============================================================================
+# Stage 3: Test image - runs validation tests
+# ============================================================================
+FROM builder AS test
+
+# Create test directory
+WORKDIR /test
+
+# Run test commands from the conda recipe
+RUN echo "Running SeqSero2S tests..." && \
+    /opt/conda/envs/seqsero2s/bin/SeqSero2S.py -h && \
+    echo "SeqSero2S.py -h: PASSED" && \
+    /opt/conda/envs/seqsero2s/bin/blastn -help && \
+    echo "blastn -help: PASSED" && \
+    /opt/conda/envs/seqsero2s/bin/SalmID.py -h && \
+    echo "SalmID.py -h: PASSED" && \
+    /opt/conda/envs/seqsero2s/bin/mlst -h && \
+    echo "mlst -h: PASSED" && \
+    echo "All tests completed successfully!"
+
+# Default command shows test results
+CMD ["echo", "All SeqSero2S tests passed successfully!"]
+
+# ============================================================================
+# Stage 4: Production/Distribution image - minimal runtime (DEFAULT)
+# ============================================================================
+FROM condaforge/mambaforge:latest AS dist
+
+# Copy conda environment from builder
+COPY --from=builder /opt/conda/envs/seqsero2s /opt/conda/envs/seqsero2s
+
+# Update PATH to use the conda environment
+ENV PATH=/opt/conda/envs/seqsero2s/bin:$PATH \
+    CONDA_DEFAULT_ENV=seqsero2s \
+    CONDA_PREFIX=/opt/conda/envs/seqsero2s
+
+# Install minimal runtime dependencies
+RUN apt-get update && \
+    apt-get install -y --no-install-recommends \
+        ca-certificates \
+        procps \
+    && apt-get clean && \
+    rm -rf /var/lib/apt/lists/* /tmp/* /var/tmp/*
+
+# Create working directory
+WORKDIR /data
+
+# Create non-root user for running the application
+RUN useradd -m -u 1000 -s /bin/bash seqsero2s && \
+    chown -R seqsero2s:seqsero2s /data
+
+USER seqsero2s
+
+# Add metadata labels
+LABEL org.opencontainers.image.version="1.1.4" \
+      org.opencontainers.image.authors="LSTUGA" \
+      org.opencontainers.image.url="https://github.com/LSTUGA/SeqSero2S" \
+      org.opencontainers.image.documentation="https://github.com/LSTUGA/SeqSero2S" \
+      org.opencontainers.image.source="https://github.com/LSTUGA/SeqSero2S" \
+      org.opencontainers.image.licenses="GPL-2.0-or-later" \
+      org.opencontainers.image.title="SeqSero2S" \
+      org.opencontainers.image.description="Simplified Salmonella serotype prediction from genome sequencing data"
+
+# No entrypoint or command for dist target