from ubuntu:latest

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

# Install package needed
RUN apt-get install -y \
        python3 \
        python3-pip \
        wget \
        git \
        libdatetime-perl \
        libxml-simple-perl \
        libdigest-md5-perl \
        default-jre \
        bioperl

# Update pip
RUN pip3 install --upgrade pip


# Install mafft 7.313
RUN rm /usr/bin/mafft  # remove mafft installed with bioperl
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 &&\
    make install