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Dockerfile
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FROM continuumio/anaconda3:2022.10
LABEL "author"="Mathieu Fourment"
LABEL "company"="University of Technology Sydney"
RUN apt-get update && \
apt-get install -y --no-install-recommends \
ant \
autoconf \
automake \
build-essential \
cmake \
default-jdk \
git \
libgsl0-dev \
libtool \
pkg-config \
unzip \
wget \
&& apt-get clean \
&& rm -rf /var/lib/apt/lists/*
RUN git clone https://github.com/beagle-dev/beagle-lib.git /beagle-lib
RUN git -C /beagle-lib checkout hmc-clock
RUN cmake -S /beagle-lib/ -B /beagle-lib/build -DBUILD_CUDA=OFF -DBUILD_OPENCL=OFF
RUN cmake --build beagle-lib/build/ --target install
RUN git clone https://github.com/4ment/beast-mcmc.git /beast-mcmc
RUN cd /beast-mcmc && git checkout torchtree-experiments && ant linux
RUN chmod +x /beast-mcmc/release/Linux/BEASTv1.10.5pre/bin/beast \
&& ln -s /beast-mcmc/release/Linux/BEASTv1.10.5pre/bin/beast /usr/local/bin/
RUN wget https://github.com/iqtree/iqtree2/releases/download/v2.2.2.6/iqtree-2.2.2.6-Linux.tar.gz
RUN tar -xzvf iqtree-2.2.2.6-Linux.tar.gz && chmod +x /iqtree-2.2.2.6-Linux/bin/iqtree2 \
&& ln -s /iqtree-2.2.2.6-Linux/bin/iqtree2 /usr/local/bin/
RUN wget https://github.com/tothuhien/lsd2/releases/download/v.2.3/lsd2_unix \
&& chmod +x lsd2_unix && mv lsd2_unix /usr/local/bin/lsd2
RUN git clone https://github.com/4ment/physher.git /physher
RUN cmake -S /physher -B /physher/build -DBUILD_CPP_WRAPPER=on -DBUILD_TESTING=on
RUN cmake --build /physher/build/ --target install
# autodiff programs
RUN git clone https://github.com/4ment/torchtree /torchtree
RUN pip install torch==1.12.1 numpy==1.22 /torchtree \
&& torchtree --help
ENV LD_LIBRARY_PATH=$LD_LIBRARY_PATH:/usr/local/lib
ENV LIBRARY_PATH=$LIBRARY_PATH:/usr/local/lib
RUN git clone https://github.com/4ment/torchtree-physher /torchtree-physher
RUN pip install /torchtree-physher
RUN pip install torchtree-scipy=1.0.0