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Dockerfile
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FROM debian:11
WORKDIR /HAMLETE
COPY . hamlete/
ADD models/* /HAMLETE/hamlete/models/
RUN chmod +x /HAMLETE/hamlete/hamleTE.py
ENV HAMLETE_DIR /HAMLETE/hamlete
ENV PATH $HAMLETE_DIR:$PATH
RUN apt update && apt install -y make build-essential libssl-dev zlib1g-dev \
libbz2-dev libreadline-dev libsqlite3-dev wget curl llvm libncurses5-dev \
libncursesw5-dev xz-utils tk-dev libffi-dev liblzma-dev python3-openssl \
git curl dh-autoreconf
RUN curl https://pyenv.run | bash
RUN echo 'export PYENV_ROOT="$HOME/.pyenv"' >> ~/.bashrc && \
echo 'export PATH="$PYENV_ROOT/bin:$PATH"' >> ~/.bashrc && \
echo 'eval "$(pyenv init -)"' >> ~/.bashrc
ENV SHELL /bin/bash
ENV PYENV_ROOT $HOME/.pyenv
ENV PATH $PYENV_ROOT/shims:$PYENV_ROOT/bin:$PATH
RUN ["/root/.pyenv/bin/pyenv","install","3.10.12"]
RUN ["/root/.pyenv/bin/pyenv","global","3.10.12"]
RUN ["python3","-m","pip","install","-r","/HAMLETE/hamlete/requirements.txt"]
RUN git clone https://github.com/BioinformaticsToolsmith/Red.git && \
cd Red/src_2.0 && sed -i '/^CXX/ s/g++-8/g++/' Makefile && \
make bin && make && \
ln -s /HAMLETE/Red/bin/Red /usr/local/bin/
RUN wget https://github.com/torognes/vsearch/archive/v2.27.0.tar.gz && \
tar xzf v2.27.0.tar.gz && \
cd vsearch-2.27.0 && \
./autogen.sh && \
./configure CFLAGS="-O3" CXXFLAGS="-O3" && \
make && \
make install