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Dockerfile
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FROM debian:bookworm-slim AS binary
LABEL authors="Erik Garrison, Simon Heumos, Andrea Guarracino"
LABEL description="Preliminary docker image containing all requirements for pggb pipeline"
LABEL base_image="debian:bookworm-slim"
LABEL software="pggb"
LABEL about.home="https://github.com/pangenome/pggb"
LABEL about.license="SPDX:MIT"
# dependencies
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
git \
bash \
cmake \
make \
g++-11 \
python3-dev \
python3-pip \
python3-venv \
pybind11-dev \
libbz2-dev \
bc \
libatomic-ops-dev \
autoconf \
libgsl-dev \
zlib1g-dev \
libzstd-dev \
libjemalloc-dev \
libhts-dev \
build-essential \
pkg-config \
time \
curl \
pigz \
tabix \
samtools \
wget \
pip \
libcairo2-dev \
unzip \
parallel \
r-base \
libclang-dev \
&& apt-get clean \
&& apt-get purge \
&& rm -rf /var/lib/apt/lists/*
# current bcftools
RUN wget https://github.com/samtools/bcftools/releases/download/1.19/bcftools-1.19.tar.bz2 \
&& tar xjf bcftools-1.19.tar.bz2 \
&& cd bcftools-1.19/ && ./configure --prefix=/usr/local/bin/ && make && make install && export PATH=/usr/local/bin/bin:$PATH && cd .. && cp /usr/local/bin/bin/* /usr/local/bin/
RUN git clone --recursive https://github.com/waveygang/wfmash \
&& cd wfmash \
&& git pull \
&& git checkout 517e1bc5c133ecac483a8479c5403f8a13d0fdd5 \
&& git submodule update --init --recursive \
&& sed -i 's/-march=native/-march=sandybridge/g' src/common/wflign/deps/WFA2-lib/Makefile \
&& cmake -H. -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' -Bbuild && cmake --build build -- -j $(nproc) \
&& cp build/bin/wfmash /usr/local/bin/wfmash \
# Libraries aren't getting installed
&& cp build/lib/* /usr/local/lib/ \
&& cd ../ \
&& rm -rf wfmash
RUN git clone --recursive https://github.com/ekg/seqwish \
&& cd seqwish \
&& git pull \
&& git checkout 0eb6468be0814ab5a0cda10d12aa38cb87d086f1 \
&& git submodule update --init --recursive \
&& cmake -H. -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' -Bbuild && cmake --build build -- -j $(nproc) \
&& cp bin/seqwish /usr/local/bin/seqwish \
&& cd ../ \
&& rm -rf seqwish
RUN git clone --recursive https://github.com/pangenome/smoothxg \
&& cd smoothxg \
&& git pull \
&& git checkout e93c62356b33c2f6db727452328e09a33bfc82c6 \
&& git submodule update --init --recursive \
&& sed -i 's/-msse4.1/-march=sandybridge -Ofast/g' deps/spoa/CMakeLists.txt \
&& sed -i 's/-march=native/-march=sandybridge -Ofast/g' deps/spoa/CMakeLists.txt \
&& sed -i 's/-march=native/-march=sandybridge -Ofast/g' deps/abPOA/CMakeLists.txt \
&& cmake -H. -DCMAKE_BUILD_TYPE=Generic -DEXTRA_FLAGS='-march=sandybridge -Ofast' -Bbuild && cmake --build build -- -j $(nproc) \
&& cp bin/smoothxg /usr/local/bin/smoothxg \
&& cp deps/odgi/bin/odgi /usr/local/bin/odgi \
&& cd ../ \
&& rm -rf odgi
# Rust
RUN curl https://sh.rustup.rs -sSf | sh -s -- -y
ENV PATH="/root/.cargo/bin:${PATH}"
RUN cargo --help
RUN git clone https://github.com/marschall-lab/GFAffix.git \
&& cd GFAffix \
&& git pull \
&& git checkout a366a94a8d7a2ffbba8978cdbcd071a9b8a03bec \
&& cargo install --force --path . \
&& mv /root/.cargo/bin/gfaffix /usr/local/bin/gfaffix \
&& cd ../ \
&& rm -rf GFAffix
RUN wget https://github.com/vgteam/vg/releases/download/v1.59.0/vg && chmod +x vg && mv vg /usr/local/bin/vg
RUN git clone https://github.com/pangenome/vcfbub \
&& cd vcfbub \
&& git pull \
&& git checkout db7775f63eab6891acb6000dddfa320146cd7c56 \
&& cargo install --force --path . \
&& mv /root/.cargo/bin/vcfbub /usr/local/bin/vcfbub \
&& cd ../ \
&& rm -rf vcfbub
RUN git clone --recursive https://github.com/vcflib/vcflib.git \
&& cd vcflib \
&& git checkout 0272f2d8ebcb70ca9b7f23a0aed3991e0a63ae6b \
&& mkdir -p build \
&& cd build \
&& cmake -DZIG=OFF -DCMAKE_BUILD_TYPE=Debug -DWFA_GITMODULE=ON .. && cmake --build . -- -j $(nproc) \
&& mv vcfwave /usr/local/bin/vcfwave \
&& mv vcfuniq /usr/local/bin/vcfuniq \
&& cd ../ \
&& rm -rf vcflib
# Additional tools
RUN git clone https://github.com/ekg/fastix.git \
&& cd fastix \
&& git pull \
&& git checkout 331c1159ea16625ee79d1a82522e800c99206834 \
&& cargo install --force --path . && \
mv /root/.cargo/bin/fastix /usr/local/bin/fastix \
&& cd ../ \
&& rm -rf fastix
RUN git clone https://github.com/ekg/pafplot.git \
&& cd pafplot \
&& git pull \
&& git checkout 7dda24c0aeba8556b600d53d748ae3103ec85501 \
&& cargo install --force --path . \
&& mv /root/.cargo/bin/pafplot /usr/local/bin/ \
&& cd ../ \
&& rm -rf pafplot
COPY pggb /usr/local/bin/pggb
RUN chmod 777 /usr/local/bin/pggb
COPY partition-before-pggb /usr/local/bin/partition-before-pggb
RUN chmod a+rx /usr/local/bin/partition-before-pggb
# MUMMER adjustments
RUN wget https://github.com/mummer4/mummer/releases/download/v4.0.0rc1/mummer-4.0.0rc1.tar.gz \
&& tar -xf mummer-4.0.0rc1.tar.gz && cd mummer-4.0.0rc1 && ./configure && make && make install && cd ../
RUN ldconfig
RUN wget https://github.com/RealTimeGenomics/rtg-tools/releases/download/3.12.1/rtg-tools-3.12.1-linux-x64.zip \
&& unzip rtg-tools-3.12.1-linux-x64.zip && sed -i 's/read -r -p "Would you like to enable automatic usage logging (y\/n)? " REPLY/REPLY="n"/g' /rtg-tools-3.12.1/rtg \
&& ln -s /rtg-tools-3.12.1/rtg /usr/local/bin/ && rtg help
# Install R package
RUN wget https://cran.r-project.org/src/contrib/Archive/data.table/data.table_1.15.2.tar.gz \
&& R CMD INSTALL data.table_1.15.2.tar.gz \
&& rm data.table_1.15.2.tar.gz
RUN wget https://github.com/arq5x/bedtools2/releases/download/v2.31.0/bedtools.static \
&& mv bedtools.static /usr/local/bin/bedtools \
&& chmod +x /usr/local/bin/bedtools
# Set up Python virtual environment
RUN python3 -m venv /opt/venv
ENV PATH="/opt/venv/bin:$PATH"
# Install Python packages in virtual environment
RUN pip install multiqc==1.22.2 \
&& pip install igraph==0.11.5 \
&& pip install pycairo==1.26.1
# copy required scripts
COPY scripts/* /usr/local/bin/
COPY scripts /usr/local/bin/scripts/
# Hacky-way to easily get versioning info
COPY .git /usr/local/bin/
SHELL ["/bin/bash", "-c"]