I am running GATK in clusters via pbs scheduling, and found "AnalyzeCovariates" could not use customized Rscript path.
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:
lsb_release -i|cut -c17-20 == 'Cent' ] ; then
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?