[BioC] Bioconductor on a Rocks cluster

[Seth Falcon]

Hi Patrick,

"Patrick Durham" <patrickd at crab.org> writes:
> Hello,
>
> I'm trying to find information about running Bioconductor in a clustered
> environment (specifically Rocks).  I've searched Google and the mailing
> list and I haven't found much at all.  I am interested in hearing from
> anyone who is successfully running Bioconductor on a cluster.  My first
> question is whether or not it will actually run on a cluster.  If so I'd
> would appreciate any links or documents you could forward to me on a
> clustered implementation.

I'm not sure Bioconductor is enough of a coehesive whole ask a
question like "does Bioconductor run on a cluster"?

But in general, R and Bioconductor packages will run on a cluster --
meaning you should be able to launch an R process that makes use of
Bioconductor packages on a given cluster node.  How much this helps
you will depend on what you are trying to do.

There are a few packages that help you do parallel computations (a
good example is MLInterfaces, I believe).  But at present, most BioC
packages won't parallelize without some custom coding effort.

+ seth

-- 
Seth Falcon | Computational Biology | Fred Hutchinson Cancer Research Center
http://bioconductor.org