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

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# Install packages needed and update pip
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RUN apt-get install -y \
        wget \
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        python3 \
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        python3-pip
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# Upgrade pip
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RUN pip3 install --upgrade pip

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# Update makeblastdb and blastp for prokka
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WORKDIR /install_dir
RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/2.10.1/ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
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    tar zxvpf ncbi-blast-2.10.1+-x64-linux.tar.gz &&\
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    cp /install_dir/ncbi-blast-2.10.1+/bin/makeblastdb /usr/local/bin/ &&\
    cp /install_dir/ncbi-blast-2.10.1+/bin/blastp /usr/local/bin/ &&\
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    rm ncbi-blast-2.10.1+-x64-linux.tar.gz
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# Install prokka:
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WORKDIR /install_dir
RUN DEBIAN_FRONTEND="noninteractive" apt install -y\
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        libdatetime-perl \
        libxml-simple-perl \
        libdigest-md5-perl \
        git \
        default-jre \
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        bioperl
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RUN echo yes | cpan Bio::Perl
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RUN git clone https://github.com/tseemann/prokka.git
RUN /install_dir/prokka/bin/prokka --setupdb &&\
    ln -s /install_dir/prokka/bin/prokka /usr/local/bin

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# Install quicktree
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WORKDIR /install_dir
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RUN git clone https://github.com/tseemann/quicktree
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WORKDIR /install_dir/quicktree
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RUN make &&\
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    ln -s /install_dir/quicktree/quicktree /usr/local/bin