R lib dependencies in the toolshed
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 $output_dir/k2n.txt fi "k2n.R" suppressMessages(require(RNAprobR)) I always get the following error: In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'RNAprobR' A solution to the problem could be to pass the R library path of the RNAprobR module or the installation folder of package "RNAprobR" as a parameter to the bash wrapper and then the k2n.R script but I can't seem to be able to do it. Do you have any suggestions? Regards, Nikos
Hi Nikos, can you provide us your tool_dependencies.xml file please? Thanks, Bjoern Am 11.02.2015 um 17:27 schrieb Nikos Sidiropoulos:
Hi all,
I have a package repository that installs an R package and another repository with a set of tools that use that package repository.
Tools that use an Rscript command interpreter load that module successfully, e.g.:
"normalize.xml"
<requirements> <requirement type="package" version="3.1.1">R_3_1_1</requirement> <requirement type="R-module">RNAprobR</requirement> <requirement type="package" version="1.0.0">RNAprobR</requirement> <requirement type="set_environment">RNA_PROBING_SCRIPT_PATH</requirement> </requirements>
<command interpreter="Rscript"> normalize.R
.... </command>
"normalize.R"
suppressMessages(require(RNAprobR))
...
But there is a tool which executes an Rscript indirectly, meaning:
"summarize_unique_barcodes.sh"
<requirements> <requirement type="package" version="4.1.0">gnu_awk</requirement> <requirement type="package" version="0.1.19">samtools</requirement> <requirement type="package" version="3.1.1">R_3_1_1</requirement> <requirement type="R-module">RNAprobR</requirement> <requirement type="package" version="1.0.0">RNAprobR</requirement> <requirement type="set_environment">RNA_PROBING_SCRIPT_PATH</requirement> </requirements>
<command interpreter="bash"> summarize_unique_barcodes.sh
...
-r \$RNA_PROBING_SCRIPT_PATH </command>
"summarize_unique_barcodes.sh"
....
#Produce k2n file
if [ "$k2n" == "True" ]; then Rscript $R_SCRIPT_PATH/k2n.R merged_temp.gz $output_dir/unique_barcodes.txt $output_dir/k2n.txt fi
"k2n.R" suppressMessages(require(RNAprobR))
I always get the following error:
In library(package, lib.loc = lib.loc, character.only = TRUE, logical.return = TRUE, : there is no package called 'RNAprobR'
A solution to the problem could be to pass the R library path of the RNAprobR module or the installation folder of package "RNAprobR" as a parameter to the bash wrapper and then the k2n.R script but I can't seem to be able to do it.
Do you have any suggestions?
Regards, Nikos ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/
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Hi Björn, Sorry for the late reply. I wasn't subscribed to the list when I sent the message and didn't receive your reply but found it here. (http://osdir.com/ml/general/2015-02/msg15128.html) Here is the tool_dependencies.xml <?xml version="1.0"?> <tool_dependency> <package name="gnu_awk" version="4.1.0"> <repository changeset_revision="cbe9f1c8c98b" name="package_gnu_awk_4_1_0" owner="iuc"/> </package> <package name="samtools" version="0.1.19"> <repository changeset_revision="632f1a03db92" name="package_samtools_0_1_19" owner="iuc"/> </package> <package name="R_3_1_1" version="3.1.1"> <repository changeset_revision="d9964efbfbe3" name="package_r_3_1_1" owner="fubar"/> </package> <package name="RNAprobR" version="1.0.0"> <repository changeset_revision="0455dc195eea" name="package_rna_probing_0_99_0" owner="nikos"/> </package> <set_environment version="1.0"> <environment_variable name="RNA_PROBING_SCRIPT_PATH" action="set_to">$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
participants (2)
-
Björn Grüning -
Nikos Sidiropoulos