soymintc/battenberg repository overview

FROM soymintc/allelecount
# refered to: https://github.com/openanalytics/r-base/blob/master/Dockerfile by Tobias Verbeke <[email protected]>

# enable apt-get use and disable tzdata interaction
USER root
ARG DEBIAN_FRONTEND=noninteractive

# For R
RUN apt-get install -y ca-certificates apt-transport-https wget locales apt-utils \
gsfonts gnupg2 libcurl4-openssl-dev libssl-dev libssh2-1-dev libxml2-dev zlib1g-dev curl

# For Rhtslib
RUN apt-get install -y libbz2-dev liblzma-dev

# Configure default locale, see https://github.com/rocker-org/rocker/issues/19
RUN echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen \
&& locale-gen en_US.utf8 \
&& /usr/sbin/update-locale LANG=en_US.UTF-8
ENV LC_ALL en_US.UTF-8
ENV LANG en_US.UTF-8
RUN echo "deb https://cloud.r-project.org/bin/linux/ubuntu focal-cran40/" > /etc/apt/sources.list.d/cran.list

# note the proxy for gpg
RUN apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
ENV R_BASE_VERSION 4.2
# 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
RUN apt-get update \
&& apt-get install -y --no-install-recommends \
littler \
r-cran-littler \
r-base=${R_BASE_VERSION}* \
r-base-core=${R_BASE_VERSION}* \
r-base-dev=${R_BASE_VERSION}* \
        r-recommended=${R_BASE_VERSION}* \
&& echo 'options(repos = c(CRAN = "https://cloud.r-project.org/"), download.file.method = "libcurl")' >> /etc/R/Rprofile.site \
&& echo 'source("/etc/R/Rprofile.site")' >> /etc/littler.r \
&& ln -s /usr/share/doc/littler/examples/install.r /usr/local/bin/install.r \
&& ln -s /usr/share/doc/littler/examples/install2.r /usr/local/bin/install2.r \
&& ln -s /usr/share/doc/littler/examples/installGithub.r /usr/local/bin/installGithub.r \
&& ln -s /usr/share/doc/littler/examples/testInstalled.r /usr/local/bin/testInstalled.r \
&& install.r docopt \
&& rm -rf /tmp/downloaded_packages/ /tmp/*.rds

# For devtools
RUN apt-get install -y libfontconfig1-dev
RUN apt-get install -y libharfbuzz-dev libfribidi-dev
RUN apt-get install -y  libfreetype6-dev libpng-dev libtiff5-dev libjpeg-dev

# Install R package managers
RUN R -e "install.packages(c('ragg', 'pkgdown', 'devtools', 'testthat', 'BiocManager', 'optparse'))"

# Battenberg prerequisites
RUN R -e "BiocManager::install('GenomicRanges')"
RUN R -e "BiocManager::install('VariantAnnotation')"
RUN R -q -e 'devtools::install_github("VanLoo-lab/ascat/ASCAT")'
RUN R -e "BiocManager::install('igordot/copynumber')"
RUN R -q -e 'devtools::install_github("Wedge-Oxford/battenberg")'