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

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 http://www.rocksclusters.org/roll-documentation/base/5.3 /customization-adding-packages.html 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: source("http://bioconductor.org/biocLite.R") biocLite(<yourpackagehere>) It sounds like others have done the same: https://lists.sdsc.edu/pipermail/npaci-rocks- discussion/2007-September/027232.html 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >