HPSCC setup

Table of Contents

1 Introduction

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.

2 Announcements and help

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).

3 What is there

3.1 R

This includes many versions of R as well as R-devel. R-devel is built every morning at 6am and all installed packages are updated. Depending on the R release schedule, other versions of R may be updated daily at the same time.

The specific setup file is setup.R.sh. It is included in setup.all.sh.

3.2 ShortRead Tools

This includes

  • bowtie
  • bwa
  • maq
  • samtools
  • tophat
  • cufflinks
  • BOOST (dependency)

and possibly other programs as needed.

If a new version has been released for one of these tools, and we do not have it installed, please contact bithelp@jhsph.edu or khansen@jhsph.edu to get it fixed. It is probably because we did not notice it.

The specific setup file is setup.shortread.sh. It is included in setup.all.sh.

3.3 Utils

This includes

  • Subversion
  • Mercurial
  • XZ utils

The specific setup file is setup.utils.sh. It is included in setup.all.sh.

3.4 Libraries

This includes

  • Boost
  • NetCDF
  • Eigen

The specific setup file is setup.libraries.sh. It is included in setup.all.sh.

3.5 Emacs 24

Including ESS, Orgmode and AUCTeX in their latest versions

The specific setup file is setup.emacs.sh. It is not included in setup.all.sh.

4 How to use it

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

5 About the R installation

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.

6 Installing R packages as a user (not administrator)

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.

Date: 2013-03-20 21:40:44 EDT

Author: Kasper Hansen

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