vinujose/ubuntu:r

$ singularity pull shub://vinujose/ubuntu:r

Singularity Recipe

Bootstrap: docker
From: ubuntu:18.04

%environment
export LC_ALL=C

%post
# Install R installation dependencies
# libssl-dev for gnupg; libcurl4-openssl-dev for Rcurl; libxml2-dev for XML; libhdf5-dev for Seurat

apt-get -y update
apt-get -y install libssl-dev libcurl4-openssl-dev libxml2-dev libhdf5-dev gnupg ca-certificates wget

# Install R
echo "deb https://cloud.r-project.org/bin/linux/ubuntu bionic-cran35/" >> /etc/apt/sources.list
gpg --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys E298A3A825C0D65DFD57CBB651716619E084DAB9
gpg -a --export E298A3A825C0D65DFD57CBB651716619E084DAB9 | apt-key add -

apt-get -y update
DEBIAN_FRONTEND=noninteractive apt-get -y install r-base
DEBIAN_FRONTEND=noninteractive apt-get -y install r-base-dev
R --slave -e 'if (!requireNamespace("BiocManager", quietly = TRUE)){ install.packages("BiocManager")}; BiocManager::install(pkgs=c("affy","limma","sva"), version = "3.8")'
echo 'install.packages(pkgs=c("reshape2", "ggplot2", "gplots", "RColorBrewer","Seurat" ))' | R --slave


%runscript
exec echo "I am a singularity container with Ubuntu 18.04 and R 3.5."

%labels
Maintainer Vinu Jose

%help
Container with Ubuntu 18.04 and R 3.5.

Collection

• Name: vinujose/ubuntu
• License: None

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