Dockerfile.base

FROM perl:5

# Install system dependencies
# With BLAST dependencies
RUN apt-get update \
  && apt-get install -y --no-install-recommends \
    less \
    locales \
    wget \
    git \
    ca-certificates \
    fonts-texgyre \
    cmake \
    autoconf \
    automake \
    make \
    gcc \
    zlib1g-dev \
    libbz2-dev \
    liblzma-dev \
    libcurl4-gnutls-dev \
    libssl-dev \
    libghc-bzlib-dev \
    libncurses5-dev \
    zlib1g-dev \
    cpanminus \
    libdist-zilla-perl \
    ncbi-blast+

WORKDIR /tmp

# Installing samtools
ENV SAMTOOLS_VERSION 1.9
RUN wget -q https://github.com/samtools/samtools/releases/download/${SAMTOOLS_VERSION}/samtools-${SAMTOOLS_VERSION}.tar.bz2 \
  && tar xfj samtools-${SAMTOOLS_VERSION}.tar.bz2 \
  && cd samtools-${SAMTOOLS_VERSION} \
  && ./configure --prefix=/usr \
  && make && make install

# Installing gsnap
ENV GSNAP_VERSION 2018-05-30
RUN wget -q http://research-pub.gene.com/gmap/src/gmap-gsnap-${GSNAP_VERSION}.tar.gz \
  && tar -xzf gmap-gsnap-${GSNAP_VERSION}.tar.gz \
  && cd gmap-${GSNAP_VERSION} \
  && ./configure --prefix=/usr \
  && make && make install

# Installing star
ENV STAR_VERSION 2.6.1b
RUN wget -q https://github.com/alexdobin/STAR/archive/${STAR_VERSION}.tar.gz \
  && tar -xzf ${STAR_VERSION}.tar.gz \
  && cd STAR-${STAR_VERSION}/source \
  && make STAR && mv STAR /usr/bin


# Installing R
ENV R_BASE_VERSION 3.3.3
## Now install R and littler, and create a link for littler in /usr/local/bin
## Also set a default CRAN repo, and make sure littler knows about it too
## Also install stringr to make dococt install (from source) easier
RUN apt-get update \
  && apt-get install -y --no-install-recommends \
    littler \
    r-cran-littler \
    r-cran-stringr \
    r-base=${R_BASE_VERSION}-* \
    r-base-dev=${R_BASE_VERSION}-* \
    r-recommended=${R_BASE_VERSION}-* \
      && echo 'options(repos = c(CRAN = "https://cloud.r-project.org/"))' >> /etc/R/Rprofile.site \
      && echo 'source("/etc/R/Rprofile.site")' >> /etc/littler.r \
  && ln -s /usr/lib/R/site-library/littler/examples/install.r /usr/local/bin/install.r \
  && ln -s /usr/lib/R/site-library/littler/examples/install2.r /usr/local/bin/install2.r \
  && ln -s /usr/lib/R/site-library/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
  && ln -s /usr/lib/R/site-library/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
  && install.r docopt \
  && rm -rf /tmp/downloaded_packages/ /tmp/*.rds \
&& rm -rf /var/lib/apt/lists/*

# Installing R dependencies
COPY install_r_packages.R .
RUN Rscript install_r_packages.R

RUN apt-get clean && rm -rf /var/lib/apt/lists/* /tmp/*

ENV LC_ALL C

WORKDIR /root