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Commit 6f261f76 authored by Peng Lian's avatar Peng Lian
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Add R-4.2.2

parent ba40b7a6
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FROM centos:centos7
LABEL CONTAINER_VERSION="0.0.2" \
AUTHOR="Peng Lian" \
EMAIL="biohpc-help@utsouthwestern.edu"
# build-time varialbes
ARG http_proxy=http://proxy.swmed.edu:3128/
ARG https_proxy=http://proxy.swmed.edu:3128/
ARG no_proxy="*.swmed.edu,*.swmed.org,*.utsouthwestern.edu,localhost,127.0.0.1/8"
ENV http_proxy="${http_proxy}" \
https_proxy="${https_proxy}" \
no_proxy="${no_proxy}"
# Configure default locale
ENV LC_ALL=en_US.UTF-8 \
LANG=en_US.UTF-8 \
R_VERSION=4.2.2
# Enable EPEL and install dependencies for building R packages
RUN mkdir /astrocyte /apps /home1 /home2 /work /project /archive /cm /programs && \
yum -y update && \
yum install -y epel-release && \
yum groupinstall -y "Development Tools" && \
yum clean all
# Enable EPEL and install dependencies for building R packages
RUN yum -y update && \
yum install -y epel-release && \
yum groupinstall -y "Development Tools" && \
yum install -y \
openssl \
openssl-devel \
libcurl \
libcurl-devel \
libpng-devel \
libxml2 \
libxml2-devel \
nlopt nlopt-devel \
boost \
boost-devel \
boost-system \
boost-filesystem \
boost-thread \
cairo-devel \
tcl-devel \
tk-devel \
wget \
python-devel \
gsl-devel \
udunits2-devel \
libpng-devel \
cairo-devel \
libtiff-devel \
fftw-devel \
freetype-devel \
cmake \
librsvg2-devel \
mariadb-devel \
pandoc \
pandoc-citeproc \
udunits-devel \
v8-314-devel \
zlib-devel \
texlive-latex \
# required by 'devtools' of R
harfbuzz-devel \
fribidi-devel \
libjpeg-turbo-devel \
&& \
yum clean all
# Install R and packagesRUN yum -y update && \
RUN yum -y update && \
yum install -y epel-release && \
yum -y install https://cdn.rstudio.com/r/centos-7/pkgs/R-${R_VERSION}-1-1.x86_64.rpm && \
yum clean all && \
ln -s /opt/R/${R_VERSION}/bin/R /usr/local/bin/R && \
ln -s /opt/R/${R_VERSION}/bin/Rscript /usr/local/bin/Rscript && \
/usr/local/bin/R -e "install.packages(c('BiocManager', 'shiny', 'shinyFiles', 'devtools'), repos='https://cloud.r-project.org')" && \
R --version
# set default CRAN mirror
COPY Rprofile.site /opt/R/${R_VERSION}/lib/R/etc/
# Default command
CMD ["R"]
options(repos = c(CRAN = 'https://cloud.r-project.org'), download.file.method = 'libcurl')
options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')
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