[BioC] Installation on a cluster

[Sean Davis]

On Thu, Apr 17, 2008 at 9:16 AM, Daniel Davidson <danield at igb.uiuc.edu> wrote:
> Hello,
>
>  I have been tasked with getting Bioconductor installed on our cluster.
>  Because the slave nodes cannot access the Internet, the normal method of
>  install using:
>
>  source("http://bioconductor.org/biocLite.R")
>  biocinstallPkgGroups("lite")
>
>  will not work.  Does anyone have a good method of doing this on a cluster?  We have a local Bioconductor mirror on the cluster that is shared of NFS.
>

Hi, Dan.

The way we do this is to make an nfs-shared /usr/local and install R
there.  Then, use biocLite to install packages to the shared
directory.    The benefit of this setup is that you update in only one
place and only once either packages or R itself and it is
automatically seen on all machines.  An added benefit is that
additional packages (graphviz, netcdf, etc.) need only be installed
into the shared /usr/local tree and all nodes will see them.  Of
course, this assumes that your nodes are all one architecture, but
since you said "cluster", I assume that is the case

Sean