[BioC] bioconductor on rocks cluster

David Schruth dschruth at u.washington.edu
Wed Jun 30 21:37:29 CEST 2010

We use R on our Rocks Cluster.

R was installed across our compute nodes by folding its RPM into a rocks 
distro compute node (re)-build 

We install our *libraries*, however,  manually & one-at-a-time into 
/share/apps/ via the root user
(who's R_LIBS variable points to the R_LIBS_SITE which points to 
/share/apps/R/site_library  which is

mounted on all nodes


For bioconductor packages we use BiocLite.
Just log in as root, fire up R, and run:


It sounds like others have done the same:

I suppose that you could install a the entire Bioconductor RPM in the 
same way we installed R (using a global node rebuild)  but that's 
probably overkill.

Anybody else have other ideas?

David M. Schruth
Informatics Consultant
Center for Environmental Genomics
University of Washington

Bryan Hepworth wrote:
> Hi All
> I'm curious to know if anyone has done a bioconductor install onto a rocks cluster at all. I'd like to know your experience and a how-to if you have managed to do so.
> Thanks
> Bryan
> Bryan Hepworth
> Assistant Institute Computing Officer
> Institute of Human Genetics
> Newcastle University
> International Centre for Life
> Newcastle
> NE1 3BZ
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