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spatial_eye_bootstrap
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Bootstrap: debootstrap
OSVersion: xenial
MirrorURL: http://us.archive.ubuntu.com/ubuntu/
IncludeCmd: apt-get
%labels
Maintainer [email protected]
Version 1.0
%environment
SHELL=/bin/bash
export SHELL
%post
#------------
#Update tools
#------------
echo "deb http://archive.ubuntu.com/ubuntu xenial main multiverse universe restricted" >> /etc/apt/sources.list
echo "deb http://archive.ubuntu.com/ubuntu xenial-updates main multiverse universe restricted" >> /etc/apt/sources.list
echo "deb http://archive.ubuntu.com/ubuntu xenial-backports main multiverse universe restricted" >> /etc/apt/sources.list
apt-get -y install software-properties-common
add-apt-repository ppa:ubuntu-toolchain-r/test
apt-get -y update
apt-get -y upgrade
apt-get -y install wget git libcurl4-openssl-dev libssl-dev libssh2-1-dev libxml2 libxml2-dev
apt-get -y install build-essential fort77 xorg-dev liblzma-dev libblas-dev gfortran gcc-multilib gobjc++ aptitude libreadline-dev libcairo2-dev libbz2-dev
#-------------------
#Add CRAN to sources
#-------------------
gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9
gpg -a --export E084DAB9 | apt-key add -
#---------
#Install R
#---------
wget https://cran.r-project.org/src/base/R-3/R-3.4.0.tar.gz
tar -zxvf R-3.4.0.tar.gz
rm R-3.4.0.tar.gz
cd R-3.4.0
./configure --prefix=/usr/local
make
make install
#--------------------
#Download Spatial Eye
#--------------------
cd /home
git clone https://github.com/jbergenstrahle/SpatialEye.git
R --vanilla <<EOF
install.packages("devtools", repos="http://cran.us.r-project.org")
install.packages(c("igraph", "leaflet.extras"), repos="http://cran.us.r-project.org")
source("https://bioconductor.org/biocLite.R")
biocLite(c("DESeq2", "annotate", "biomaRt", "AnnotationDb1", "org.Hs.eg.db", "org.Mm.eg.db", "genefilter", "scatter", "scran", "edgeR", "threejs", "cowplot"))
devtools::install("SpatialEye")
q()
EOF
chmod -R 777 /home/SpatialEye