Dockerfile

FROM ubuntu:18.04
LABEL author="Rodrigo Martin <rodrigo.martin@bsc.es>"

ARG DEBIAN_FRONTEND=noninteractive
RUN export DEBIAN_FRONTEND=noninteractive

# Install dependencies
RUN apt-get update && \
    apt-get install -y \
    autoconf \
    build-essential \
    bzip2 \
    cmake \
    cython \
    git \
    libbz2-dev \
    libncurses5-dev \
    openjdk-8-jdk \
    pkg-config \                    
    python \
    python2.7 \
    python2.7-dev \                    
    python-setuptools \
    python-pip \
    python-psutil \                    
    python-numpy \
    python-pandas \
    python-distribute \
    python-pysam \
    python-scipy \                    
    software-properties-common \
    libz-dev \
    libglib2.0-dev \
    libbz2-dev \
    liblzma-dev \
    default-jre \
    autoconf \
    wget \
    python3 \
    python3-pip \
    git \
    zlib1g-dev && \
    apt-get clean -y

# Copy the source code
RUN mkdir -p /opt/prepy-wrapper/src
COPY ./src /opt/prepy-wrapper/src
# Change the permissions to be able to execute the scripts in src folder
RUN chmod -R 755 /opt/prepy-wrapper/src
COPY ./requirements.txt /opt/prepy-wrapper/requirements.txt
ENV PATH $PATH:/opt/prepy-wrapper/src

# Install dependencies
RUN pip3 install -r /opt/prepy-wrapper/requirements.txt

# Install hap.py
RUN git clone --recurse-submodules https://github.com/Illumina/hap.py
WORKDIR /hap.py

RUN pip install bx-python

# copy git repository into the image
RUN mkdir -p /opt/hap.py-source
RUN cp -r /hap.py/* /opt/hap.py-source/

# make minimal HG19 reference sequence
RUN mkdir -p /opt/hap.py-data

# download HG19 reference data
WORKDIR /opt/hap.py-data

# get + install ant
WORKDIR /opt
RUN wget http://archive.apache.org/dist/ant/binaries/apache-ant-1.9.7-bin.tar.gz && \
    tar xzf apache-ant-1.9.7-bin.tar.gz && \
    rm apache-ant-1.9.7-bin.tar.gz
ENV PATH $PATH:/opt/apache-ant-1.9.7/bin

# run hap.py installer in the image, don't run tests since we don't have a reference file
WORKDIR /opt/hap.py-source
RUN python install.py /opt/hap.py --with-rtgtools --no-tests
WORKDIR /opt/hap.py

# run basic tests
RUN bin/test_haplotypes

# remove source folder
WORKDIR /
RUN rm -rf /opt/hap.py-source

# Add pre.py to path
ENV PATH $PATH:/opt/hap.py/bin