On Mon, Apr 28, 2014 at 2:40 PM, Hans-Rudolf Hotz hrh@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