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# Kalign Downstream Benchmark Container
#
# Extends the base benchmark setup with tools for downstream application
# benchmarks: positive selection (HyPhy), phylogenetics (IQ-TREE),
# homology detection (HMMER), and confidence comparison (GUIDANCE2).
#
# Build:
# podman build -f Containerfile.downstream -t kalign-downstream .
#
# Run all downstream benchmarks:
# podman run -it \
# -v ./benchmarks/data:/kalign/benchmarks/data \
# -v ./benchmarks/results:/kalign/benchmarks/results \
# kalign-downstream \
# python -m benchmarks.downstream --all -j 4
#
# Quick smoke test (5 cases per pipeline):
# podman run -it \
# -v ./benchmarks/data:/kalign/benchmarks/data \
# -v ./benchmarks/results:/kalign/benchmarks/results \
# kalign-downstream \
# python -m benchmarks.downstream --all -j 4 --quick
#
# Generate figures from existing results:
# podman run -it \
# -v ./benchmarks/results:/kalign/benchmarks/results \
# -v ./benchmarks/figures:/kalign/benchmarks/figures \
# kalign-downstream \
# python -m benchmarks.downstream --figures -o benchmarks/figures/
FROM ubuntu:24.04
ENV DEBIAN_FRONTEND=noninteractive
# ── System dependencies ──────────────────────────────────────────────
RUN apt-get update && apt-get install -y --no-install-recommends \
build-essential cmake g++ git curl wget ca-certificates \
python3 python3-pip python3-venv python3-dev \
pkg-config zlib1g-dev libcurl4-openssl-dev libssl-dev libeigen3-dev libboost-dev \
clustalo mafft hmmer \
perl libwww-perl libbio-perl-perl cpanminus \
&& rm -rf /var/lib/apt/lists/*
# Bio::Perl convenience module (removed from BioPerl core in 1.7.x)
RUN cpanm --notest Bio::Perl
# ── MUSCLE v5 from source ───────────────────────────────────────────
# myutils.h checks __arm64__ (macOS) but not __aarch64__ (Linux); add it
RUN cd /tmp && \
git clone --depth 1 https://github.com/rcedgar/muscle.git && \
cd muscle/src && \
sed -i 's/defined(__arm64__)/defined(__arm64__) || defined(__aarch64__)/' myutils.h && \
bash build_linux.bash && \
cp ../bin/muscle /usr/local/bin/ && \
rm -rf /tmp/muscle
# ── INDELible v1.03 from source ─────────────────────────────────────
RUN cd /tmp && \
git clone --depth 1 https://github.com/matsengrp/indelible.git && \
cd indelible/src && \
make && \
cp indelible /usr/local/bin/ && \
rm -rf /tmp/indelible
# ── HyPhy from source ───────────────────────────────────────────────
RUN cd /tmp && \
git clone --depth 1 https://github.com/veg/hyphy.git && \
cd hyphy && \
cmake -DCMAKE_BUILD_TYPE=Release -DNOAVX=ON . && \
make -j"$(nproc)" hyphy && \
cp hyphy /usr/local/bin/hyphy && \
cp -r res /usr/local/lib/hyphy && \
rm -rf /tmp/hyphy
ENV HYPHY_LIB=/usr/local/lib/hyphy
ENV HYPHY_PATH=/usr/local/lib/hyphy
# ── IQ-TREE 2 from source ───────────────────────────────────────────
RUN cd /tmp && \
git clone --depth 1 --recurse-submodules https://github.com/iqtree/iqtree2.git && \
cd iqtree2 && \
mkdir build && cd build && \
cmake -DCMAKE_BUILD_TYPE=Release .. && \
make -j"$(nproc)" && \
cp iqtree2 /usr/local/bin/ && \
rm -rf /tmp/iqtree2
# ── GUIDANCE2 from GitHub (original tar.gz URL is dead) ────────────
# guidance.pl uses FindBin-relative paths ($Bin, $Bin/../Selecton, etc.)
# We install the full www/ tree under /opt/guidance-root/ so sibling
# directories (Selecton, bioSequence_scripts_and_constants) resolve
# correctly relative to the guidance.pl script location.
RUN cd /tmp && \
git clone --depth 1 https://github.com/anzaika/guidance.git && \
cd guidance && make && \
mkdir -p /opt/guidance-root && \
cp -r www/Guidance /opt/guidance-root/Guidance && \
cp -r www/Selecton /opt/guidance-root/Selecton && \
cp -r www/bioSequence_scripts_and_constants /opt/guidance-root/bioSequence_scripts_and_constants && \
mkdir -p /opt/guidance-root/Guidance/exec && \
cp programs/msa_set_score/msa_set_score /opt/guidance-root/Guidance/exec/ && \
cp programs/removeTaxa/removeTaxa /opt/guidance-root/Guidance/exec/ && \
cp programs/isEqualTree/isEqualTree /opt/guidance-root/Guidance/exec/ && \
chmod +x /opt/guidance-root/Guidance/guidance.pl && \
mkdir -p /opt/programs/semphy /opt/programs/msa_set_score \
/opt/programs/removeTaxa /opt/programs/isEqualTree && \
cp programs/semphy/semphy /opt/programs/semphy/ && \
cp programs/msa_set_score/msa_set_score /opt/programs/msa_set_score/ && \
cp programs/removeTaxa/removeTaxa /opt/programs/removeTaxa/ && \
cp programs/isEqualTree/isEqualTree /opt/programs/isEqualTree/ && \
printf '#!/bin/sh\nexec perl /opt/guidance-root/Guidance/guidance.pl "$@"\n' \
> /usr/local/bin/guidance2 && \
chmod +x /usr/local/bin/guidance2 && \
rm -rf /tmp/guidance
# ── Kalign C build ──────────────────────────────────────────────────
COPY . /kalign
WORKDIR /kalign
RUN mkdir -p build && cd build && \
cmake -DCMAKE_BUILD_TYPE=Release .. && \
make -j"$(nproc)"
# ── Record tool versions at build time ──────────────────────────────
RUN echo "build_date=$(date -u +%Y-%m-%dT%H:%M:%SZ)" > /tool_versions.txt && \
echo "kalign=$(build/src/kalign --version 2>&1 | head -1 || echo unknown)" >> /tool_versions.txt && \
echo "mafft=$(mafft --version 2>&1 | head -1 || echo unknown)" >> /tool_versions.txt && \
echo "muscle=$(muscle --version 2>&1 | head -1 || echo unknown)" >> /tool_versions.txt && \
echo "clustalo=$(clustalo --version 2>&1 | head -1 || echo unknown)" >> /tool_versions.txt && \
echo "hmmer=$(hmmbuild -h 2>&1 | grep '^# HMMER' | head -1 || echo unknown)" >> /tool_versions.txt && \
echo "iqtree=$(iqtree2 --version 2>&1 | grep 'IQ-TREE' | head -1 || echo unknown)" >> /tool_versions.txt && \
echo "indelible=1.03" >> /tool_versions.txt && \
echo "hyphy=$(hyphy --version 2>&1 | head -1 || echo unknown)" >> /tool_versions.txt
# ── Python environment ──────────────────────────────────────────────
RUN python3 -m venv /venv
ENV PATH="/venv/bin:/kalign/build/src:$PATH"
RUN pip install --no-cache-dir uv && \
uv pip install --no-cache -e ".[benchmark]" && \
uv pip install --no-cache \
dendropy biopython pandas matplotlib scipy seaborn numpy
# ── Verify tools ────────────────────────────────────────────────────
RUN which kalign && which clustalo && which mafft && which muscle && \
which hmmbuild && which hmmsearch && which iqtree2 && \
which hyphy && which indelible && which guidance2
# ── Data & results directories ──────────────────────────────────────
RUN mkdir -p benchmarks/data/downloads/pfam_seed \
benchmarks/data/downloads/swissprot \
benchmarks/data/downloads/selectome \
benchmarks/results/calibration \
benchmarks/results/positive_selection \
benchmarks/results/phylo_accuracy \
benchmarks/results/hmmer_detection \
benchmarks/figures
EXPOSE 8050
CMD ["python", "-m", "benchmarks.downstream", "--help"]
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