Re: [galaxy-dev] R lib dependencies in the toolshed

14 Feb 2015

      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.sidiro@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