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from ubuntu:20.04
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# Update apt-get packages
RUN apt-get update &&\
    apt-get -y upgrade

# Install package needed
RUN apt-get install -y \
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        python3 \
        python3-pip \
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        wget \
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        git

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# Update pip
RUN pip3 install --upgrade pip

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# Install packages to install mafft
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RUN DEBIAN_FRONTEND="noninteractive" apt-get install -y \
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        libdatetime-perl                 \
        libxml-simple-perl \
        libdigest-md5-perl \
        default-jre \
        bioperl
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# Install mafft 7.313
RUN rm /usr/bin/mafft  # remove mafft installed with bioperl
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WORKDIR /install_dir
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RUN wget https://mafft.cbrc.jp/alignment/software/mafft-7.313-with-extensions-src.tgz &&\
    tar xf mafft-7.313-with-extensions-src.tgz &&\
    rm mafft-7.313-with-extensions-src.tgz
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WORKDIR /install_dir/mafft-7.313-with-extensions/core
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RUN make clean &&\
    make &&\
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    make install