Hi all, I have a package repository that installs an R package and another repository with a set of tools that use that package repository. Tools that use an Rscript command interpreter load that module successfully, e.g.: "normalize.xml" <requirements> <requirement type="package" version="3.1.1">R_3_1_1</requirement> <requirement type="R-module">RNAprobR</requirement> <requirement type="package" version="1.0.0">RNAprobR</requirement> <requirement type="set_environment">RNA_PROBING_SCRIPT_PATH</requirement> </requirements> <command interpreter="Rscript"> normalize.R .... </command> "normalize.R" suppressMessages(require(RNAprobR)) ... But there is a tool which executes an Rscript indirectly, meaning: "summarize_unique_barcodes.sh" <requirements> <requirement type="package" version="4.1.0">gnu_awk</requirement> <requirement type="package" version="0.1.19">samtools</requirement> <requirement type="package" version="3.1.1">R_3_1_1</requirement> <requirement type="R-module">RNAprobR</requirement> <requirement type="package" version="1.0.0">RNAprobR</requirement> <requirement type="set_environment">RNA_PROBING_SCRIPT_PATH</requirement> </requirements> <command interpreter="bash"> summarize_unique_barcodes.sh ... -r \$RNA_PROBING_SCRIPT_PATH </command> "summarize_unique_barcodes.sh" .... #Produce k2n file if [ "$k2n" == "True" ]; then Rscript $R_SCRIPT_PATH/k2n.R merged_temp.gz $output_dir/unique_barcodes.txt $output_dir/k2n.txt fi "k2n.R" suppressMessages(require(RNAprobR)) I always get the following error: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'RNAprobR' A solution to the problem could be to pass the R library path of the RNAprobR module or the installation folder of package "RNAprobR" as a parameter to the bash wrapper and then the k2n.R script but I can't seem to be able to do it. Do you have any suggestions? Regards, Nikos