https://github.com/ctlab/phantasus
Raw File
Tip revision: 80c7b427b73eabcf1cbf64adf47708e2640d3ffb authored by Nitesh Turaga on 29 October 2019, 17:11 UTC
bump x.y.z version to even y prior to creation of RELEASE_3_10 branch
Tip revision: 80c7b42
Dockerfile
FROM ubuntu:16.04

ARG TARGET_BRANCH=master
ARG PHANTASUS_BUILD
ARG GITHUB_PAT
ENV OCPU_MASTER_HOME=/var/phantasus/ocpu-root

RUN apt-get -y update && \
    apt-get -y dist-upgrade && \
    apt-get -y install \
        software-properties-common \
        git \
        libcairo2-dev \
        libxt-dev \
        libssl-dev \
        libssh2-1-dev \
        libcurl4-openssl-dev \
        nginx \
        libapparmor-dev \
        libxml2-dev \
        locales \
        wget


RUN add-apt-repository -y 'deb http://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/' && apt-get -y update
RUN apt-get install -y --allow-unauthenticated r-base r-base-dev

RUN apt-add-repository -y 'deb http://ppa.launchpad.net/maarten-fonville/protobuf/ubuntu zesty main' && \
    apt-get -y update

RUN apt-get -y --allow-unauthenticated install \
    libprotobuf-dev \
    protobuf-compiler

RUN R -e 'install.packages("protolite", repo = "https://cran.rstudio.com/")'

#RUN apt-add-repository -y ppa:opencpu/opencpu-2.0 && \
#    apt-get update && \
#    apt-get install -y --allow-unauthenticated \
#        opencpu-lib
#RUN R -e 'install.packages("opencpu", repo = "https://cran.rstudio.com/")'
#RUN sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu xenial/" >> /etc/apt/sources.list'
# protobuf 3.5, with 2GB byte limit
RUN gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
RUN gpg -a --export E084DAB9 | apt-key add -

RUN R -e 'install.packages("devtools", repo = "https://cran.rstudio.com/")'
RUN R -e 'install.packages("unix")'

#RUN git clone -b ${TARGET_BRANCH} --recursive https://github.com/ctlab/phantasus /root/phantasus
COPY . /root/phantasus

RUN R -e 'source("https://bioconductor.org/biocLite.R")'

RUN R -e 'devtools::install_github("ctlab/fgsea", tag="1.9.5")'
RUN R -e 'devtools::install("/root/phantasus", build_vignettes=T)'
RUN printf "window.PHANTASUS_BUILD='$PHANTASUS_BUILD';" >> /root/phantasus/inst/www/phantasus.js/RELEASE.js
RUN cp -r /root/phantasus/inst/www/phantasus.js /var/www/html/phantasus
RUN cp /root/phantasus/inst/configs/default /etc/nginx/sites-available/default
RUN cp /root/phantasus/inst/configs/opencpu.conf /etc/opencpu/server.conf
RUN cp /root/phantasus/inst/configs/index.html /var/www/html/
RUN rm -rf /root/phantasus/inst

EXPOSE 80

RUN locale-gen en_US.UTF-8
ENV LANG en_US.UTF-8
ENV LANGUAGE en_US:en
ENV LC_ALL en_US.UTF-8

RUN mkdir -p /var/phantasus/cache
RUN mkdir -p /var/phantasus/preloaded
RUN mkdir -p /var/phantasus/ocpu-root

CMD service nginx start && \
   R -e 'library(phantasus); servePhantasus("0.0.0.0", 8001, openInBrowser = F, cacheDir="/var/phantasus/cache", preloadedDir="/var/phantasus/preloaded")'

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