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/ > ___________________________________________________________ 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/
