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from ubuntu:18.04
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# Update apt-get packages
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RUN apt-get update &&\
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    apt-get -y upgrade

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

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# Update makeblastdb for prokka
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WORKDIR /tmp
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RUN wget ftp://ftp.ncbi.nlm.nih.gov/blast/executables/LATEST/ncbi-blast-2.10.0+-x64-linux.tar.gz &&\
    tar zxvpf ncbi-blast-2.10.0+-x64-linux.tar.gz &&\
    cp /tmp/ncbi-blast-2.10.0+/bin/makeblastdb /usr/local/bin/ &&\
    rm ncbi-blast-2.10.0+-x64-linux.tar.gz
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# Install mash
WORKDIR /tmp
RUN wget https://github.com/marbl/Mash/releases/download/v2.2/mash-Linux64-v2.2.tar &&\
    tar -xf mash-Linux64-v2.2.tar &&\
    rm mash-Linux64-v2.2.tar &&\
    mv /tmp/mash-Linux64-v2.2/mash /usr/local/bin &&\
    rm -r mash-Linux64-v2.2


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# Install barrnap
WORKDIR /tmp
RUN wget https://github.com/tseemann/barrnap/archive/0.8.tar.gz &&\
    tar -xf 0.8.tar.gz &&\
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    rm 0.8.tar.gz &&\
    mv /tmp/barrnap-0.8/bin/barrnap /usr/local/bin  &&\
    # Remove heavy useless files
    rm -r /tmp/barrnap-0.8/examples /tmp/barrnap-0.8/build/*.aln

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# Install prokka:
WORKDIR /tmp
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RUN blastp --version
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RUN apt-get install -y\
        libdatetime-perl \
        libxml-simple-perl \
        libdigest-md5-perl \
        git \
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        default-jre \
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        bioperl
RUN git clone https://github.com/tseemann/prokka.git
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RUN /tmp/prokka/bin/prokka --setupdb &&\
    ln -s /tmp/prokka/bin/prokka /usr/local/bin

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# Install MMseqs2 Version: f05f8c51d6e9c7c0b15fbd533e4b678303f50b3e
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WORKDIR /tmp
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RUN wget https://mmseqs.com/latest/mmseqs-linux-sse41.tar.gz &&\
    tar xvfz mmseqs-linux-sse41.tar.gz &&\
    rm mmseqs-linux-sse41.tar.gz &&\
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    mv /tmp/mmseqs/bin/mmseqs /usr/local/bin &&\
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    # remove useless files
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    rm -r /tmp/mmseqs
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# Install mafft 7.313
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RUN rm /usr/bin/mafft  # remove mafft installed with bioperl
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WORKDIR /tmp
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
WORKDIR /tmp/mafft-7.313-with-extensions/core
RUN make clean &&\
    make &&\
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    make install

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# Install FastTree version 2.1.11 Double precision (No SSE3)
WORKDIR /tmp
RUN wget http://www.microbesonline.org/fasttree/FastTree.c &&\
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    gcc -DOPENMP -fopenmp -DUSE_DOUBLE -Wall -O3 -finline-functions -funroll-loops -o FastTreeMP FastTree.c -lm &&\
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    ln -s /tmp/FastTreeMP /usr/local/bin
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## Install FastME FastME 2.1.6.1
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WORKDIR /tmp
RUN apt-get install -y automake  &&\
    git clone https://gite.lirmm.fr/atgc/FastME.git
WORKDIR /tmp/FastME
RUN ./configure &&\
    make &&\
    make install


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