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how to make AnalyzeCovariates use the R path in the clusters environment.

chunxuanchunxuan Member
edited January 2014 in Ask the GATK team

I am running GATK in clusters via pbs scheduling, and found "AnalyzeCovariates" could not use customized Rscript path.

More info:

All nodes have CentOS installed, R is already installed and could be found under "/usr/bin/R" from "which R". Unfortunately, R version is not identical among nodes, i.e., some nodes have R 2.15, and some have R 3.0 installed.

I installed the latest R version under my home folder, and add following commands to .bash_profile and .bash_rc:

if [ lsb_release -i|cut -c17-20 == 'Cent' ] ; then
alias R='/home/XXX/R-3.0.2/bin/R'
alias Rscript='/home/XXX/R-3.0.2/bin/Rscript'
fi

If I login to the cluster via qsub -I, and type R in the console, customized R will be invoked, and this is also shown in "which R" :

alias R='/home/XXX/R-3.0.2/bin/R'
~/R-3.0.2/bin/R

All GATK required packages have been installed.

However, when I run AnalyzeCovariates, it reported that some packages are missing, and it turns out that AnalyzeCovariates is using the R under "/usr/bin/R". So how to make AnalyzeCovariates use the right R? Do I miss something in the bash configure files?

Thanks.

Answers

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