biocyberman/singularity-r:latest
$ singularity pull shub://biocyberman/singularity-r:latest
Singularity Recipe
BootStrap: docker
From: nvidia/cuda:10.2-base-ubuntu18.04
%labels
Maintainer Jeremy Nicklas
R_Version 3.6.3
%apprun R
exec R "${@}"
%apprun Rscript
exec Rscript "${@}"
%runscript
exec R "${@}"
%post
# Software versions
export R_VERSION=3.6.3
# get rid of tzdata nagging
export DEBIAN_FRONTEND=noninteractive
# Get dependencies
apt-get update
apt-get install -y --no-install-recommends locales
# Configure default locale
echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
locale-gen en_US.utf8
/usr/sbin/update-locale LANG=en_US.UTF-8
export LC_ALL=en_US.UTF-8
export LANG=en_US.UTF-8
#install R and R packages
#specific version of R to be installed
export R_BASE_VERSION=3.6.3
#add R CRAN mirror to apt sources to install R using APT
apt-key adv --keyserver keyserver.ubuntu.com \
--recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9 && \
echo "deb https://mirrors.dotsrc.org/cran/bin/linux/ubuntu bionic-cran35/" > /etc/apt/sources.list.d/cran.list && \
apt-get update && \
apt-get -y install --no-install-recommends --no-install-suggests \
libcurl4-openssl-dev \
libssl-dev \
libxml2-dev \
libxt-dev \
libcairo2-dev \
r-base=${R_BASE_VERSION}* \
r-base-core=${R_BASE_VERSION}* \
r-cran-class \
r-cran-nnet \
r-base-dev=${R_BASE_VERSION}* \
r-base-html=${R_BASE_VERSION}* \
r-recommended=${R_BASE_VERSION}*
R -e "install.packages(c('data.table', 'tidyverse', 'rmarkdown'), Ncpus = 7)"
# Add a default CRAN mirror
echo "options(repos = c(CRAN = 'https://cran.rstudio.com/'), download.file.method = 'libcurl')" >> /usr/lib/R/etc/Rprofile.site
# Add a directory for host R libraries
mkdir -p /library
echo "R_LIBS_SITE=/library:\${R_LIBS_SITE}" >> /usr/lib/R/etc/Renviron.site
# Clean up
rm -rf /var/lib/apt/lists/*
Collection
- Name: biocyberman/singularity-r
- License: MIT License
View on Datalad
Metrics
key | value |
---|---|
id | /containers/biocyberman-singularity-r-latest |
collection name | biocyberman/singularity-r |
branch | master |
tag | latest |
commit | 34d9605cddef1c385552954d6d2d54e566d5eb2b |
version (container hash) | 29323343b539a031782cf904c63fac7e |
build date | 2020-03-30T22:17:14.631Z |
size (MB) | 973.0 |
size (bytes) | 336023583 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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