[R] Running Shell Script with R

jp134711 johnandrewpura at gmail.com
Mon Nov 28 17:10:01 CET 2011

I'm having some trouble getting my shell script to work. I've checked out the
Intro to R Manual and a host of other websites, but I still can't get the
script to work when I submit the job to the cluster.

Here is my main R code:

##Load Libraries

## Load Time Data
Args <- commandArgs(trailingOnly = TRUE);
timeDat <- read.flowSet(files=NULL, path=Args[1]);
save(timeDat,file = Args[2]);

Here is my shell script file

#$ -cwd
#$ -q all.q

R --slave --vanilla --file="/home/jpura/Desktop/FDA_Trial_Data/testscript.R"
--args "/home/jpura/Desktop/FDA_Trial_Data/Experiment_1/"

It runs just fine (i.e. I get the right output file, which is
testscript.RData) when I type the lines in the shell script file directly
into the command prompt. However, when I try to submit the file using:

qsub "path/to/testscript.sh", I don't get the desired output file.

Any insights to this is be greatly appreciated.


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