Instructions to install R Modules on Dalma

In order to install R packages, we need to access the internet to download a script. During an interactive session on Dalma, R does not have access to bioconductor. So we will install the R packages on the login node and then start an interactive session to start the analysis.

First load the relevant modules and start R.

Now we can source the bioconductor site to install the packages we are interested in. Note that the first time you do this, R will ask you if you want to setup a personal library. You must say yes. You don’t have permission to make changes to system wide R library.

The packages needed for RNA-seq module. Before you start installing you can first check if the module is already available by running the library() command. Below the commands are assuming that none of the packages are installed. At the end of the installation message, you will get a message to update old packages, just type “n” for no.

Now we have to quit ( no need to save the workspace ) start an interactive session and start R again.