====== R, RStudio server and Bioconductor ======

  * R is a free software environment for statistical computing and graphics. ([[http://www.r-project.org/|site]])

Add to /etc/apt/sources.list this line:
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<code>
deb http://cran.mirror.garr.it/mirrors/CRAN/bin/linux/ubuntu precise/
</code>
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then
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<code>
sudo apt-key adv --keyserver keyserver.ubuntu.com --recv-keys E084DAB9
sudo apt-get update
sudo apt-get install r-base
</code>
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Enter R at prompt:
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<code>
R version 3.0.1 (2013-05-16) -- "Good Sport"
Copyright (C) 2013 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
</code>
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\\
  * RStudio IDE is a powerful and productive user interface for R. It’s free and open source. ([[http://www.rstudio.com|site]])
Download and install
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<code>
apt-get install gdebi-core
apt-get install libapparmor1

wget http://download2.rstudio.org/rstudio-server-0.97.551-amd64.deb
gdebi rstudio-server-0.97.551-amd64.deb
</code>
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Configure reverse-proxy
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<code>
apt-get install libapache2-mod-proxy-html
apt-get install libxml2-dev
a2enmod proxy
a2enmod proxy_http
nano -w /etc/apache2/sites-enabled/000-default
</code>
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<code>
  <Proxy *>
    Allow from localhost
  </Proxy>

  ProxyPass        /rstudio/ http://localhost:8787/
  ProxyPassReverse /rstudio/ http://localhost:8787/
  RedirectMatch permanent ^/rstudio$ /rstudio/
</code>
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<code>
service apache2 restart
</code>
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Limit connection from localhost
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<code>
nano -w /etc/rstudio/rserver.conf
</code>
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<code>
  www-address=127.0.0.1
</code>
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<code>
rstudio-server stop
rstudio-server start
</code>
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\\
  * Bioconductor provides tools for the analysis and comprehension of high-throughput genomic data. Bioconductor uses the R statistical programming language, and is open source and open development. ([[http://www.bioconductor.org/|Site]])
Additional packages required
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<code>
apt-get install libcurl4-openssl-dev
</code>
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Login as root and at R prompt:
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<code>
source("http://bioconductor.org/biocLite.R")
biocLite()
biocLite(c("GenomicFeatures", "AnnotationDbi"))
</code>
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