Dear Peter, that is very very helpful, many thanks for your suggestions ;) !
On Tue, Jul 11, 2017 at 11:34 PM, Anthoni, Peter (IMK) <
peter.anth...@kit.edu> wrote:
> Hi,
>
> The problem is most likely, you need to call a R CMD BATCH with your
> arguments and the R-script inside of a shell script
Hi,
The problem is most likely, you need to call a R CMD BATCH with your arguments
and the R-script inside of a shell script that you submit to your qsub.
Unfortunately we don't use qsub anymore so can't test it, but it should be as
follows:
R-script eg. test.R:
> ##First read in the arguments
This sounds like an operating system specific question, in that "submit the R
script to a PBS HPC scheduler" would be the kind of action that would run R
with very different environment variables and possibly different access
credentials than your usual interactive terminal. A thorough reading
Dear all,
please could you advise me on the following : I've written a R script that
reads 3 arguments from the command line, i.e. :
" args <- commandArgs(TRUE)
TUMOR <- args[1]
GERMLINE <- args[2]
CHR <- args[3] ".
when I submit the R script to a PBS HPC scheduler, I do the following
(below), b
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