R lib dependencies in the toolshed

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R lib dependencies in the toolshed

Nikos Sidiropoulos
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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Re: R lib dependencies in the toolshed

Björn Grüning-3
Hi Nikos,

can you provide us your tool_dependencies.xml file please?

Thanks,
Bjoern

Am 11.02.2015 um 17:27 schrieb Nikos Sidiropoulos:

> 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
> ___________________________________________________________
> Please keep all replies on the list by using "reply all"
> in your mail client.  To manage your subscriptions to this
> and other Galaxy lists, please use the interface at:
>   https://lists.galaxyproject.org/
>
> To search Galaxy mailing lists use the unified search at:
>   http://galaxyproject.org/search/mailinglists/
>
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Re: R lib dependencies in the toolshed

Nikos Sidiropoulos
In reply to this post by Nikos Sidiropoulos
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 <[hidden email]> 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
___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/