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Singularity_recipev2.R3.5
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Singularity_recipev2.R3.5
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BootStrap: shub
From: shub://pranithavangala/singularity:0_part1
%labels
AUTHOR Elisa Donnard
Version v2.0
%environment
export SRC=/usr/local/src
export BIN=/usr/local/bin
export R_VERSION=R-3.5.0
%apprun R
exec R "$@"
%apprun Rscript
exec Rscript "$@"
%runscript
exec R "$@"
%post
######
## vim
######
apt-get install -y vim
#####
## R
#####
export SRC=/usr/local/src
export BIN=/usr/local/bin
export R_VERSION=R-3.5.0
%post
NPROCS=`awk '/^processor/ {s+=1}; END{print s}' /proc/cpuinfo`
wget https://cran.rstudio.com/src/base/R-3/R-3.5.0.tar.gz
tar xvf R-3.5.0.tar.gz
cd R-3.5.0
apt-get update
apt-get install -y libblas3 libblas-dev liblapack-dev liblapack3 curl
apt-get install -y libgmp10 libgmp-dev
apt-get install -y gcc fort77 aptitude
aptitude install -y g++
aptitude install -y xorg-dev
aptitude install -y libreadline-dev
aptitude install -y gfortran
gfortran --version
apt install -y libssl-dev libxml2-dev libpcre3-dev liblzma-dev libbz2-dev libcurl4-openssl-dev
apt-get update
./configure --enable-R-static-lib --with-blas --with-lapack --enable-R-shlib=yes
echo "Will use make with $NPROCS cores."
make -j${NPROCS}
make install
echo install.packages\(\"devtools\"\, repos\=\'https://cloud.r-project.org\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"ade4\"\, repos\=\'https://cloud.r-project.org\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"ape\"\, repos\=\'https://cloud.r-project.org/\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"FD\"\, repos\=\'https://cloud.r-project.org/\'\, Ncpus\=${NPROCS}\) | R --slave
echo install.packages\(\"ggplot2\"\, repos\=\'https://cloud.r-project.org/\'\, Ncpus\=${NPROCS}\) | R --slave
R --slave -e "source('https://bioconductor.org/biocLite.R'); \
biocLite()"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('tidyverse')"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('edgeR')"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('DESeq2')"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('gplots')"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('Biobase', dep = TRUE)"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('DropletUtils', dep = TRUE)"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('stringr', dep = TRUE)"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('densityClust', dep = TRUE)"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('RColorBrewer', dep = TRUE)"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('Rtsne', dep = TRUE)"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('ggpubr', dep = TRUE)"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('limSolve', dep = TRUE)"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('scran', dep = TRUE)"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('fpc', dep = TRUE)"
R --slave -e "source('https://bioconductor.org/biocLite.R'); biocLite('irlba', dep = TRUE)"
R --slave -e "devtools::install_github('garber-lab/SignallingSingleCell')"
###################
# mount directories
mkdir /project /nl /share /.nextflow /amazon