Dockerfile

from ubuntu:16.04

# Update apt-get packages
RUN apt-get update &&\
    apt-get -y upgrade

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

# Update pip
RUN pip3 install --upgrade pip

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

RUN rm /usr/bin/mafft  # remove mafft installed with bioperl

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