HPSCC setup

The HPSCC will be a collection of software for the Biostat cluster maintained by a group of non-sysadmins. It includes R, tools for high-throughput sequencing and additional utilities.

Announcements regarding this set of tools is send to the bit-help email list. It is a very good idea to subscribe to this list to be up to date with what is happening. Contact Marvin for subscription.

Questions should preferably be sent to bithelp@jhsph.edu, or perhaps to Kasper Daniel Hansen (khansen@jhsph.edu).

Inside the directory /hpscc/usr/local/setup/ (on the cluster) are a number of files of the format setup.*.sh. Each of these files contains commands to set up the appropriate suite of programs (such that setup.R.sh contains the information to set up R). By setup we mean specifying the right paths for executing programs, searching man/info pages, linking etc.

Each of these files simply needs to be sourced in order to work (an example in the next paragraph).

One file is special: setup.all.sh which makes a "standard" setup (including all future programs we install). If you are willing to trust us, all you need to do is to include the following lines of code inside your .bashrc file in your home directory:

if [ -f /hpscc/usr/local/setup/setup.all.sh ]; then
    source  /hpscc/usr/local/setup/setup.all.sh
fi

R will always point to the latest stable release. There will also be R-$(VERSION) for specific versions of R as well as R-devel.

R-devel (and its installed packages) is updated daily at 6am east coast time. In fact, you might be running R-devel on the cluster while we update it. This might crash your R-devel session (although we have not seen this happen ever). But consider yourself warned and do not complain if you lose work.

R (the stable version) will seldom be updated (probably around every time a minor version is released). Its packages will also be updated seldom, although it happens occasionally as bug fixes are released (if you need a package to be updated, contact us).

R will no longer run on enigma2. If you are running R inside of Emacs using ESS, and you are unable to start R (and you are constantly being prompted for the start directory) you are probably running on enigma2.

If you have an R package you want to use, and you believe there is even the smallest chance that someone else is interested, the easiest is to ask to get it installed system-wide. Email khansen@jhsph.edu.

Otherwise, you should be able to use install.packages() and R CMD INSTALL out of the box. This requires that you are NOT setting RLIBS in your .bash_rc nor using .libPaths() in your .Rproile.

Please note that installing R packages is version specific, so you need to install it on every version you use.