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Dockerfile
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ARG UBUNTU_VERSION=16
FROM ubuntu:16.04 AS base-16
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
bzip2 \
default-jre \
git \
perl-base \
php7.0-cli \
php7.0-xml \
php7.0-mysql \
python-matplotlib \
python-numpy \
python-pysam \
r-base-core \
r-cran-optparse \
r-cran-robustbase \
r-cran-foreach \
r-cran-doparallel \
r-cran-mass \
tabix \
unzip \
wget
FROM ubuntu:18.04 AS base-18
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
bzip2 \
default-jre \
git \
perl-base \
php7.2-cli \
php7.2-xml \
php7.2-mysql \
python-matplotlib \
python-numpy \
python-pysam \
r-base-core \
r-cran-optparse \
r-cran-robustbase \
r-cran-foreach \
r-cran-doparallel \
r-cran-mass \
tabix \
unzip \
wget
FROM base-${UBUNTU_VERSION} AS tools-ubuntu-16
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
build-essential \
cmake \
cpanminus \
libbz2-dev \
liblzma-dev \
libncurses5-dev \
libpng-dev \
libmysqlclient-dev \
libqt5sql5-mysql \
libqt5xmlpatterns5-dev \
libssl-dev \
qt5-default \
qt5-qmake \
qtbase5-dev
FROM base-${UBUNTU_VERSION} AS tools-ubuntu-18
RUN apt-get update && DEBIAN_FRONTEND=noninteractive apt-get -y install \
build-essential \
cmake \
cpanminus \
libbz2-dev \
liblzma-dev \
libmysqlclient-dev \
libncurses5-dev \
libqt5sql5-mysql \
libpng-dev \
libqt5xmlpatterns5-dev \
libssl-dev \
qt5-default \
qt5-qmake \
qtbase5-dev
FROM tools-ubuntu-${UBUNTU_VERSION} AS build
ADD . /megSAP
WORKDIR /megSAP/data
RUN chmod 755 download_*.sh && ./download_tools.sh
FROM base-${UBUNTU_VERSION}
COPY --from=build /megSAP/ /megSAP/
COPY --from=build /megSAP/data/dbs/ /megSAP/data/dbs_static/
COPY --from=build /usr/local/share/perl/ /usr/local/share/perl/
COPY --from=build /usr/local/lib/x86_64-linux-gnu/perl/ /usr/local/lib/x86_64-linux-gnu/perl/
COPY --from=build /usr/local/bin/ /usr/local/bin/
WORKDIR /megSAP
ENTRYPOINT ["/bin/bash"]