Dockerfile

# Test on automated build
# Base image
FROM ubuntu:16.04

# Set default shell
SHELL ["/bin/bash", "-c"]

# Init
USER root

# Update base image
RUN apt-get update && \
  apt-get upgrade -y

# Install dependencies
RUN apt-get install -y --no-install-recommends \
        bzip2 \
        php7.0-mysql \
        ca-certificates \
        cmake \
        less \
        gcc \
        rsync \
        zlib1g-dev \
        debconf-utils \
        g++ \
        libncurses5-dev \
        libqt5xmlpatterns5-dev \
        libqt5sql5-mysql \
        make \
        git \
        php \
        php7.0-xml \
        python \
        python-matplotlib \
        python-software-properties \
        qt5-default \
        software-properties-common \
        tabix \
        unzip \
        nano \
        wget \
	libbz2-dev \
	liblzma-dev


# Install Java from custom repository
# Note that this auto-accepts the license terms
RUN add-apt-repository ppa:webupd8team/java && \
	apt-get update && \
	echo "oracle-java8-installer shared/accepted-oracle-license-v1-1 select true" | debconf-set-selections && \
	apt-get install -y --no-install-recommends oracle-java8-installer oracle-java8-set-default

# Install and configure megSAP
RUN cd / && \
        git clone https://github.com/sbilge/megSAP.git && \ 
  cd /megSAP && cp settings.ini.default settings.ini && \
        cd /megSAP/data && \
        /bin/bash download_tools.sh && \
        /bin/bash download_tools_somatic.sh 

RUN chmod -R 777 megSAP

# Configure mount points
RUN cd /megSAP/data && \
  mv dbs dbs_old && \
  mv genomes genomes_old && \
  ln -s /mnt/data/dbs  && \
  ln -s /mnt/data/genomes