Hi Björn,

Sorry for the late reply. I wasn't subscribed to the list when I sent
the message and didn't receive your reply but found it here.
(http://osdir.com/ml/general/2015-02/msg15128.html)

Here is the tool_dependencies.xml

<?xml version="1.0"?>

<tool_dependency>
    <package name="gnu_awk" version="4.1.0">
        <repository changeset_revision="cbe9f1c8c98b"
name="package_gnu_awk_4_1_0" owner="iuc"/>
    </package>
    <package name="samtools" version="0.1.19">
        <repository changeset_revision="632f1a03db92"
name="package_samtools_0_1_19" owner="iuc"/>
    </package>
    <package name="R_3_1_1" version="3.1.1">
        <repository changeset_revision="d9964efbfbe3"
name="package_r_3_1_1" owner="fubar"/>
    </package>
    <package name="RNAprobR" version="1.0.0">
        <repository changeset_revision="0455dc195eea"
name="package_rna_probing_0_99_0" owner="nikos"/>
    </package>
    <set_environment version="1.0">
        <environment_variable name="RNA_PROBING_SCRIPT_PATH"
action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable>
    </set_environment>
</tool_dependency>

Bests,
Nikos

On 11 February 2015 at 17:27, Nikos Sidiropoulos <nikos.sid...@gmail.com> wrote:
> 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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