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
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