On Mon, Apr 28, 2014 at 2:40 PM, Hans-Rudolf Hotz <h...@fmi.ch> wrote: > On 04/28/2014 03:32 PM, Bradley Belfiore wrote: >> >> Thank you for your quick response, my command tag is: >> <command> >> interpreter="bash">Rscript_wrapper.sh >> /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata >> $pathwayid $species $output >> </command> >> >> So I believe Im calling R via the Rscript_wrapper.sh?
There is a problem with the XML closing of the <command> tag. You appear to have a bash script calling an R script. Try: <command interpreter="bash">Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output </command> Or, if you mark your shell script as executable and include the #!/bin/bash line, you don't need the interpreter setting: <command>Rscript_wrapper.sh /Users/bbelfio1/galaxy-dist/tools/pathview/Pathview.R $genedata $pathwayid $species $output </command> Also, you should be able to use relative paths rather than that absolute path (which is not portable). Peter ___________________________________________________________ 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: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/