churchill-lab/scRATE:latest
$ singularity pull shub://churchill-lab/scRATE:latest
Singularity Recipe
BootStrap: docker
From: ubuntu:16.04
%help
This container runs R.
%labels
Maintainer Kwangbom (KB) Choi, Ph.D.
%apprun R
exec R "${@}"
%apprun Rscript
exec Rscript "${@}"
%runscript
exec R "${@}"
%post
mkdir -p /scratch/global /scratch/local /rcc/stor1/refdata /rcc/stor1/projects /rcc/stor1/depts /extR/library1 /extR/library2
apt-get update
apt-get -y install \
wget \
build-essential \
software-properties-common \
apt-transport-https \
locales \
libv8-dev \
libhdf5-serial-dev
echo "LC_ALL=en_US.UTF-8" >> /etc/environment
echo "en_US.UTF-8 UTF-8" >> /etc/locale.gen
echo "LANG=en_US.UTF-8" > /etc/locale.conf
locale-gen en_US.UTF-8
echo 'deb https://cloud.r-project.org/bin/linux/ubuntu xenial-cran35/' >> /etc/apt/sources.list
apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9 51716619E084DAB9
add-apt-repository -y "ppa:marutter/rrutter3.5"
add-apt-repository -y "ppa:marutter/c2d4u3.5"
apt-get update
apt-get -y install --no-install-recommends --allow-unauthenticated\
r-base \
r-base-core \
r-base-dev \
r-recommended \
r-base-html \
r-doc-html \
r-cran-devtools \
r-cran-rcpp \
r-cran-rcppparallel \
r-cran-bh
apt-get clean
mkdir -p $HOME/.R/
echo "CXX14FLAGS=-O3 -march=native -mtune=native -fPIC\n" >> $HOME/.R/Makevars
Rscript -e "install.packages('rstan')"
Rscript -e "install.packages('rstanarm')"
Rscript -e "install.packages('brms')"
Rscript -e "install.packages('hdf5r')"
Rscript -e "devtools::install_github('mojaveazure/loomR', ref='develop')"
Rscript -e "devtools::install_github('churchill-lab/scRATE', dep=FALSE, build_vignettes=TRUE)"
rm -rf /var/lib/apt/lists/*
echo "options(repos = c(CRAN = 'https://cloud.r-project.org/'), download.file.method = 'libcurl')" >> /usr/lib/R/etc/Rprofile.site
Collection
- Name: churchill-lab/scRATE
- License: None
View on Datalad
Metrics
key | value |
---|---|
id | /containers/churchill-lab-scRATE-latest |
collection name | churchill-lab/scRATE |
branch | master |
tag | latest |
commit | e31c6d76a12098e5a3f9573d5761f16d8013dec9 |
version (container hash) | ddb9e1af8de277699f172145b40b59b7 |
build date | 2020-08-10T06:23:45.368Z |
size (MB) | 1112.0 |
size (bytes) | 395677727 |
SIF | Download URL (please use pull with shub://) |
Datalad URL | View on Datalad |
Singularity Recipe | Singularity Recipe on Datalad |
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