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Dockerfile
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FROM rocker/tidyverse
MAINTAINER "Gregory Jefferis" jefferis@gmail.com
## System libraries
RUN apt-get update -qq && apt-get install -y --no-install-recommends \
cmake \
git \
libglu1-mesa-dev \
libhdf5-dev
RUN mkdir -p /tmp/src && cd /tmp/src \
&& git clone --depth 5 https://github.com/jefferis/cmtk \
&& cd cmtk/core && mkdir build && cd build \
&& cmake -DCMAKE_INSTALL_PREFIX:PATH=/usr/local .. \
&& make all install \
&& cd / \
&& rm -rf /tmp/src
# Java for rJava
RUN apt-get update -qq && apt-get install -y --no-install-recommends \
default-jdk \
libbz2-dev \
liblzma-dev \
&& R CMD javareconf \
install2.r rJava
# try because otherwise the stop inside selfupdate can stop the build here
RUN install2.r natmanager && r -e "try(natmanager::selfupdate())"
RUN r -e "natmanager::install('core')"
# NB we use the natverse GITHUB PAT for the update process also
RUN r -e "natmanager::install('natverse')" \
&& r -e "natverse::natverse_update(update = TRUE, upgrade = 'always', auth_token=natmanager::check_pat(create = F))"
RUN apt-get autoclean -y \
&& rm -rf /var/lib/apt/lists/*