--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/Dockerfile	Fri Mar 13 21:22:16 2026 +0000
@@ -0,0 +1,175 @@
+# =========================
+#   CSP2 for Galaxy/AWS Batch (offline Nextflow)
+# =========================
+
+# ---------- Build stage ----------
+FROM ubuntu:focal AS build
+
+ARG DEBIAN_FRONTEND=noninteractive
+ARG CSP2_VER="0.9.0"
+ARG BEDTOOLS_VER="2.31.1"
+ARG MUMMER_VER="4.0.0"
+ARG SKESA_VER="2.4.0"
+ARG MASH_VER="2.3"
+ARG BBMAP_VER="38.90"
+ARG PYTHON_VER="3.8"
+ARG SOURCEFORGE_MIRROR="psychz"
+ARG IQTREE_VER="2.0.6"
+
+# Use a stable working directory
+WORKDIR /workspace
+
+# Base build deps (include Java to verify/prewarm Nextflow here)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    tzdata gpg-agent software-properties-common build-essential \
+    zlib1g-dev libghc-bzlib-dev liblzma-dev wget ca-certificates \
+    cmake curl git xz-utils openjdk-17-jre-headless \
+ && rm -rf /var/lib/apt/lists/*
+
+# Python venv for runtime tools
+RUN add-apt-repository 'ppa:deadsnakes/ppa' && apt-get update && \
+    apt-get install -y --no-install-recommends \
+      python${PYTHON_VER} python${PYTHON_VER}-dev python${PYTHON_VER}-venv \
+ && python${PYTHON_VER} -m venv --copies /opt/venv \
+ && rm -rf /var/lib/apt/lists/*
+
+ENV PATH="/opt/venv/bin:${PATH}"
+
+# Core Python packages
+RUN pip install --no-cache-dir -U \
+    pandas~=1.2.0 pybedtools refchooser scikit-learn
+
+# ---- Fetch sources/artifacts ----
+    
+# bedtools
+ADD https://github.com/arq5x/bedtools2/archive/refs/tags/v${BEDTOOLS_VER}.tar.gz .
+# mummer
+ADD https://github.com/mummer4/mummer/releases/download/v${MUMMER_VER}rc1/mummer-${MUMMER_VER}rc1.tar.gz .
+# skesa prebuilt bins
+ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/skesa.centos.7.7 .
+ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/gfa_connector.centos7.7 .
+ADD https://github.com/ncbi/SKESA/releases/download/${SKESA_VER}/kmercounter.centos7.7 .
+# mash
+ADD https://github.com/marbl/Mash/releases/download/v${MASH_VER}/mash-Linux64-v${MASH_VER}.tar .
+# iqtree2
+ADD https://github.com/Cibiv/IQ-TREE/releases/download/v${IQTREE_VER}/iqtree-${IQTREE_VER}-Linux.tar.gz .
+
+# ---- Build/install tools into /usr/local ----
+# bedtools
+RUN tar -xzf v${BEDTOOLS_VER}.tar.gz && rm v${BEDTOOLS_VER}.tar.gz && \
+    cd bedtools2-${BEDTOOLS_VER} && make -j && make install
+
+# Install MUMmer and copy Perl modules where dnadiff expects them
+RUN tar -xvf mummer-${MUMMER_VER}rc1.tar.gz && rm mummer-${MUMMER_VER}rc1.tar.gz && \
+    cd mummer-${MUMMER_VER}rc1 && \
+    ./configure --prefix=/usr/local && make -j && make install && ldconfig && \
+    mkdir -p /usr/local/lib/mummer && cp -a scripts/*.pm /usr/local/lib/mummer/
+
+# skesa tools (rename and install)
+RUN install -m 0755 skesa.centos.7.7        /usr/local/bin/skesa && \
+    install -m 0755 gfa_connector.centos7.7 /usr/local/bin/gfa_connector && \
+    install -m 0755 kmercounter.centos7.7   /usr/local/bin/kmercounter
+
+# mash
+RUN tar -xvf mash-Linux64-v${MASH_VER}.tar && \
+    install -m 0755 mash-Linux64-v${MASH_VER}/mash /usr/local/bin/mash
+
+# bbmap (grab all scripts/binaries)
+RUN wget -O BBMap_${BBMAP_VER}.tar.gz \
+      "https://sourceforge.net/projects/bbmap/files/BBMap_${BBMAP_VER}.tar.gz/download?use_mirror=${SOURCEFORGE_MIRROR}" && \
+    tar -xvf BBMap_${BBMAP_VER}.tar.gz && \
+    cp -a bbmap/* /usr/local/bin/ && \
+    rm -rf bbmap BBMap_${BBMAP_VER}.tar.gz
+
+# iqtree2
+RUN tar -xzf iqtree-${IQTREE_VER}-Linux.tar.gz && \
+    install -m 0755 iqtree-${IQTREE_VER}-Linux/bin/iqtree2 /usr/local/bin/iqtree && \
+    rm -rf iqtree-${IQTREE_VER}-Linux iqtree-${IQTREE_VER}-Linux.tar.gz
+
+# choose a version
+ARG NXF_VER="25.04.7"
+
+# install that exact launcher & prewarm framework into /opt/nextflow
+RUN curl -fsSL -o /usr/local/bin/nextflow \
+      "https://github.com/nextflow-io/nextflow/releases/download/v${NXF_VER}/nextflow" \
+ && chmod 0755 /usr/local/bin/nextflow \
+ && mkdir -p /opt/nextflow \
+ && chmod -R a+rwX /opt/nextflow \
+ && NXF_HOME=/opt/nextflow NXF_OFFLINE=false NXF_VER=${NXF_VER} /usr/local/bin/nextflow -version \
+ && ls -l /usr/local/bin/nextflow
+
+# ---------- Runtime stage ----------
+FROM ubuntu:focal AS runtime
+
+ARG DEBIAN_FRONTEND=noninteractive
+ARG CSP2_VER="0.9.0"
+
+# Python venv for runtime tools
+# Lean runtime libs + Python3.8 + Perl (no PPAs)
+RUN apt-get update && apt-get install -y --no-install-recommends \
+    ca-certificates openjdk-17-jre-headless bash tzdata perl perl-modules-5.30 \
+    libgomp1 liblzma5 zlib1g libbz2-1.0 coreutils make curl gawk \
+    python3.8 python3.8-venv python3.8-distutils \
+ && rm -rf /var/lib/apt/lists/*
+
+# Bring over tools and Python venv
+COPY --from=build /usr/local/bin/ /usr/local/bin/
+COPY --from=build /usr/local/libexec/mummer /usr/local/libexec/mummer
+COPY --from=build /usr/local/share/ /usr/local/share/
+COPY --from=build /opt/venv /opt/venv
+
+# Bring over Nextflow launcher and baked framework cache
+COPY --from=build /usr/local/bin/nextflow /usr/local/bin/nextflow
+COPY --from=build /opt/nextflow /opt/nextflow
+
+# Ensure any UID (Galaxy user) can execute nextflow and write minimal state into the cache
+RUN chmod 0755 /usr/local/bin/nextflow \
+ && chmod -R a+rwX /opt/nextflow
+
+# Bring the modules into the runtime image (if not already)
+COPY --from=build /usr/local/lib/mummer /usr/local/lib/mummer
+
+# Bring MUMmer shared libs into the runtime image
+COPY --from=build /usr/local/lib /usr/local/lib
+
+# Make sure dynamic linker can find them
+RUN ldconfig || true
+
+# Belt-and-suspenders for minimal images
+ENV LD_LIBRARY_PATH="/usr/local/lib:${LD_LIBRARY_PATH}"
+
+# Permissions: allow any UID to read/execute the libs
+RUN chmod -R a+rX /usr/local/lib
+
+# Make modules readable by any UID; create compatibility symlink if needed
+RUN chmod -R a+rX /usr/local/lib/mummer /usr/local/libexec/mummer && \
+    test -d /usr/local/lib/mummer || ln -s /usr/local/libexec/mummer /usr/local/lib/mummer
+
+# Ensure the common mummer executables are executable by all
+RUN chmod 0755 /usr/local/bin/dnadiff /usr/local/bin/nucmer /usr/local/bin/promer /usr/local/bin/show-snps || true
+
+# Help Perl find modules regardless of layout
+ENV PERL5LIB="/usr/local/lib/mummer:/usr/local/libexec/mummer:/usr/local/share/mummer:${PERL5LIB}"
+
+# Runtime environment
+ENV PATH="/opt/venv/bin:/usr/local/bin:${PATH}" \
+    LC_ALL=C \
+    NXF_HOME=/opt/nextflow \
+    NXF_OFFLINE=true \
+    CSP2_VER=${CSP2_VER}
+
+# Install the CSP2 pipeline under /opt/csp2 (avoid /app which Galaxy mounts)
+WORKDIR /opt/csp2
+
+# Copy your pipeline (these paths must exist in the build context)
+COPY bin              ./bin
+COPY conf             ./conf
+COPY subworkflows     ./subworkflows
+COPY CSP2.nf          ./CSP2.nf
+COPY nextflow.config  ./nextflow.config
+
+# permissions for arbitrary UID
+RUN chmod -R a+rX /opt/csp2 && chmod -R a+rX /opt/nextflow
+
+# IMPORTANT: No ENTRYPOINT for Galaxy/AWS Batch. Neutral CMD.
+CMD ["/bin/bash"]