dominik-handler/AP_singu:r
$ singularity pull shub://dominik-handler/AP_singu:r
Singularity Recipe
#R in singularity
Bootstrap: docker
From: ubuntu:14.04
%runscript
"$@"
%post
apt-get update
apt-get -y install wget git sudo curl libssl-dev libxml2-dev software-properties-common libcurl4-openssl-dev
add-apt-repository universe
apt-get update
apt-get -y install pandoc
apt-get clean && apt-get update && apt-get install -y \
locales \
language-pack-fi \
language-pack-en && \
export LANGUAGE=en_US.UTF-8 && \
export LANG=en_US.UTF-8 && \
export LC_ALL=en_US.UTF-8 && \
locale-gen en_US.UTF-8 && \
dpkg-reconfigure locales
#insall R-dependencies
apt-get -y build-dep r-base
#install R
mkdir /R
cd /R
version="3.5.0"
wget http://cran.at.r-project.org/src/base/R-3/R-$version.tar.gz
tar -xzf R-$version.tar.gz
cd /R/R-$version
./configure
make
make install
apt-get clean
#install R-packages
R --slave -e 'install.packages(c( "devtools"), repos = "http://cran.wu.ac.at/") '
R --slave -e 'install.packages(c( "tidyverse", "plotly", "Cairo", "gridExtra"), repos = "http://cran.wu.ac.at/") '
R --slave -e 'options(unzip = "internal"); devtools::install_github("tidyverse/ggplot2") '
R --slave -e 'install.packages(c( "cowplot" ), repos = "http://cran.wu.ac.at/") '
R --slave -e 'source("http://bioconductor.org/biocLite.R"); biocLite("remotes"); biocLite("pachterlab/sleuth@v0.30.0")'
R --slave -e 'source("https://bioconductor.org/biocLite.R"); biocLite("rhdf5")'
#R --slave -e 'options(unzip = "internal"); devtools::install_github("dominik-handler/sleuth", ref = "master")'
R --slave -e 'source("https://bioconductor.org/biocLite.R"); biocLite("remotes"); biocLite("COMBINE-lab/wasabi")'
apt-get clean
mkdir /groups
mkdir /scratch
mkdir /scratch-ii2
mkdir /clustertmp
%test
R --version
Rscript --version
Collection
- Name: dominik-handler/AP_singu
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/dominik-handler-AP_singu-r |
collection name | dominik-handler/AP_singu |
branch | master |
tag | r |
commit | ed20f19ac3fbdce6ad9625280215d88bf6fcb8fc |
version (container hash) | 3d832ed3dcd6a6311ddacb15fc71c165 |
build date | 2019-10-18T12:26:33.072Z |
size (MB) | 2440 |
size (bytes) | 904704031 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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