Zentrum für Molekularbiologie der Pflanzen (ZMBP)

Installing Bioconductor on Ubuntu

1. Add any R mirror (see https://cran.r-project.org/mirrors.html for a list of all available mirrors) to your sources.list:

a. Open the terminal and type:

$ sudo gedit /etc/apt/sources.list

b. Then, append the address to the list that corresponds to your Ubuntu version:

· If you are operating Ubuntu 14.04 LTS (trusty):

deb cran.uni-muenster.de/bin/linux/ubuntu trusty/

· If you are operating Ubuntu 16.04 LTS (xenial):

deb cran.uni-muenster.de/bin/linux/ubuntu xenial/

c. Save and exit your sources.list


2. Now, install the latest version of R by typing in the terminal (one by one):

$ sudo apt-get update

$ sudo apt-get install r-base

$ sudo apt-get install r-base-dev

3. Open R in the terminal by typing:

$ R


4. In R, install Bioconductor (in your home directory) by entering the following commands (and accepting all proposed install locations):

source("https://bioconductor.org/biocLite.R")

biocLite()


5. Once Bioconductor has been installed, you can download additional packages and workflows via the Bioconductor download manager from within R.

Example: installing the “RNA-Seq workflow”:

a. First, open the terminal and download xml and curl libraries by typing:

$ sudo apt-get install libcurl4-openssl-dev

$ sudo apt-get install libxml2-dev

b. Then, open R in the terminal and type:

source("http://bioconductor.org/workflows.R")

workflowInstall("rnaseqGene")

Note: In step 3, if you open R as a super-user (via $ sudo R), Bioconductor (and all other R packages) will be installed outside your /home directory. Thus, you will have to open R as a super-user anytime you want to install another R package in the future.

Recommended IDE: RStudio (https://www.rstudio.com/products/rstudio/download/)