Dockerfile

# lift from cmiller R docker repo
# https://github.com/chrisamiller/docker-R
# add seurat dev repo
# add python stack 
# add umap 

FROM ubuntu:xenial

ARG R_VERSION
ARG BUILD_DATE
ARG SEURAT_VERSION=3.1.0
ENV BUILD_DATE 2019-01-18
ENV R_VERSION=${R_VERSION:-3.5.1}
RUN apt-get update && apt-get install -y --no-install-recommends locales && \
    echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen && \
    locale-gen en_US.UTF-8 && \
    LC_ALL=en_US.UTF-8 && \
    LANG=en_US.UTF-8 && \
    /usr/sbin/update-locale LANG=en_US.UTF-8 && \
    TERM=xterm && \
    apt-get install -y --no-install-recommends \
    bash-completion \
    ca-certificates \
    file \
    fonts-texgyre \
    g++ \
    gfortran \
    gsfonts \
    libbz2-1.0 \
    curl \
    libssl-dev \
    libcurl4-openssl-dev \
    libnss-sss libxml2-dev \
    python3-dev \
    python3-pip \
    libcurl3 \
    libicu55 \
    libjpeg-turbo8 \
    libopenblas-dev \
    libpangocairo-1.0-0 \
    libpcre3 \
    libpng12-0 \
    libtiff5 \
    liblzma5 \
    locales \
    zlib1g \
    libbz2-dev \
    libcairo2-dev \
    libpango1.0-dev \
    libjpeg-dev \
    libicu-dev \
    libmariadb-client-lgpl-dev \
    libmysqlclient-dev \
    libpcre3-dev \
    libpng-dev \
    libreadline-dev \
    libtiff5-dev \
    liblzma-dev \
    libx11-dev \
    libxt-dev \
    libhdf5-dev \
    perl \
    tcl8.5-dev \
    tk8.5-dev \
    texinfo \
    texlive-extra-utils \
    texlive-fonts-recommended \
    texlive-fonts-extra \
    texlive-latex-recommended \
    x11proto-core-dev \
    xauth \
    xfonts-base \
    xvfb ncurses-dev libssl-dev \
    zlib1g-dev && \
    cd /tmp/ && \
    ## Download source code
    curl -O https://cran.r-project.org/src/base/R-3/R-${R_VERSION}.tar.gz && \
    ## Extract source code
    tar -xf R-${R_VERSION}.tar.gz && \
    cd R-${R_VERSION} && \
    ## Set compiler flags
    R_PAPERSIZE=letter && \
    R_BATCHSAVE="--no-save --no-restore" && \
    R_BROWSER=xdg-open && \
    PAGER=/usr/bin/pager && \
    PERL=/usr/bin/perl && \
    R_UNZIPCMD=/usr/bin/unzip && \
    R_ZIPCMD=/usr/bin/zip && \
    R_PRINTCMD=/usr/bin/lpr && \
    LIBnn=lib && \
    AWK=/usr/bin/awk && \
    CFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" && \
    CXXFLAGS="-g -O2 -fstack-protector-strong -Wformat -Werror=format-security -Wdate-time -D_FORTIFY_SOURCE=2 -g" && \
    ## Configure options
    ./configure --enable-R-shlib \
               --enable-memory-profiling \
               --with-readline \
               --with-blas="-lopenblas" \
               --disable-nls \
               --without-recommended-packages && \
    ## Build and install
    make && \
    make install && \
    ## Add a default CRAN mirror
    echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site && \
    ## Add a library directory (for user-installed packages)
    mkdir -p /usr/local/lib/R/site-library && \
    chown root:staff /usr/local/lib/R/site-library && \
    chmod g+wx /usr/local/lib/R/site-library && \
    ## Fix library path
    echo "R_LIBS_USER='/usr/local/lib/R/site-library'" >> /usr/local/lib/R/etc/Renviron && \
    echo "R_LIBS=\${R_LIBS-'/usr/local/lib/R/site-library:/usr/local/lib/R/library:/usr/lib/R/library'}" >> /usr/local/lib/R/etc/Renviron && \
    ## install packages from date-locked MRAN snapshot of CRAN
    [ -z "$BUILD_DATE" ] && BUILD_DATE=$(TZ="America/Los_Angeles" date -I) || true && \
    MRAN=https://mran.microsoft.com/snapshot/${BUILD_DATE} && \
    echo MRAN=$MRAN >> /etc/environment && \
    export MRAN=$MRAN && \
    echo "options(repos = c(CRAN='$MRAN'), download.file.method = 'libcurl')" >> /usr/local/lib/R/etc/Rprofile.site && \
    ## Use littler installation scripts
    Rscript -e "install.packages(c('littler', 'docopt'), repo = '$MRAN')" && \
    ln -s /usr/local/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r && \
    ln -s /usr/local/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r && \
    ln -s /usr/local/lib/R/site-library/littler/bin/r /usr/local/bin/r
    
   ## install r packages, bioconductor, etc ##
   ADD install.r /tmp/
   RUN R -f /tmp/install.r 
   # RUN R -e 'install.packages(c("devtools"))'
   # RUN R -e 'devtools::install_github(repo = "satijalab/seurat", ref = "release/3.0")'
   #RUN R -f "install.packages(c("devtools"))"
   
   RUN Rscript -e "install.packages('devtools')"
   # RUN Rscript -e "devtools::install_github(repo='satijalab/seurat', ref = 'release/${SEURAT_VERSION}')" 
   RUN Rscript -e "devtools::install_github('cole-trapnell-lab/leidenbase', dep=FALSE)"
   RUN Rscript -e "devtools::install_github('cole-trapnell-lab/monocle3', dep=FALSE)"
   RUN Rscript -e "devtools::install_github(repo='diazlab/CONICS/CONICSmat', dep = FALSE)"
   
   
   # add umap
   RUN pip3 install setuptools && \
       pip3 install umap-learn
   
   ## Clean up
   RUN cd / && \
   rm -rf /tmp/* && \
   apt-get autoremove -y && \
   apt-get autoclean -y && \
   rm -rf /var/lib/apt/lists/* && \
   apt-get clean