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Bash script to set up R, install a few R packages, and get Rstudio Server running on ubuntu.
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| sudo sh -c 'echo "deb http://cran.rstudio.com/bin/linux/ubuntu trusty/" >> /etc/apt/sources.list' | |
| gpg --keyserver keyserver.ubuntu.com --recv-key E084DAB9 | |
| gpg -a --export E084DAB9 | sudo apt-key add - | |
| sudo apt-get update | |
| sudo apt-get -y install r-base libapparmor1 libcurl4-gnutls-dev libxml2-dev libssl-dev gdebi-core | |
| sudo apt-get install libcairo2-dev | |
| sudo apt-get install libxt-dev | |
| sudo apt-get install git-core | |
| sudo /bin/dd if=/dev/zero of=/var/swap.1 bs=1M count=1024 | |
| sudo /sbin/mkswap /var/swap.1 | |
| sudo /sbin/swapon /var/swap.1 | |
| sudo sh -c 'echo "/var/swap.1 swap swap defaults 0 0 " >> /etc/fstab' | |
| sudo su - -c "R -e \"install.packages('devtools', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"install.packages('Rcpp', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"install.packages('RcppEigen', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"install.packages('ggplot2', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"install.packages('Cairo', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"install.packages('evaluate', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"install.packages('formatR', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"install.packages('highr', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"install.packages('markdown', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"install.packages('yaml', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"install.packages('htmltools', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"install.packages('knitr', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"install.packages('rmarkdown', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"install.packages('RColorBrewer', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"install.packages('easypackages', repos='http://cran.rstudio.com/')\"" | |
| sudo su - -c "R -e \"source('http://bioconductor.org/biocLite.R'); biocLite('BiocParallel')\"" | |
| sudo su - -c "R -e \"source('http://bioconductor.org/biocLite.R'); biocLite('Biobase')\"" | |
| sudo su - -c "R -e \"source('http://bioconductor.org/biocLite.R'); biocLite('EBSeq')\"" | |
| sudo su - -c "R -e \"source('http://bioconductor.org/biocLite.R'); biocLite('monocle')\"" | |
| sudo su - -c "R -e \"source('http://bioconductor.org/biocLite.R'); biocLite('sincell')\"" | |
| sudo su - -c "R -e \"source('http://bioconductor.org/biocLite.R'); biocLite('scde')\"" | |
| sudo su - -c "R -e \"source('http://bioconductor.org/biocLite.R'); biocLite('scran')\"" | |
| sudo su - -c "R -e \"source('http://bioconductor.org/biocLite.R'); biocLite('scater')\"" | |
| sudo su - -c "R -e \"devtools::install_github('kdkorthauer/scDD')\"" | |
| wget https://download2.rstudio.org/rstudio-server-0.99.903-amd64.deb | |
| sudo gdebi rstudio-server-0.99.903-amd64.deb |
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Adding 'easypackages' to support Rscript scripting for environment setup