Good afternoon Galaxy list, I've got a Python script which calls an R script. When I run a job using Galaxy, I get the following output from R: Error in file(file, "r", encoding = encoding) : cannot open the connection In addition: Warning message: In file(file, "r", encoding = encoding) : cannot open file 'rocprc.R': No such file or directory The difficult thing here is that both scripts are in the same directory. I tried using os.path.realpath(PYTHON SCRIPT) to get the name of the current directory so that I could force R to operate in same; I still get this error. Telling Python to print the results from os.path.realpath(PYTHON SCRIPT) gave me "~/galaxy-dist/database/job_working_directory". Also, the Python script works perfectly when called from the command line, so I know this is a Galaxy issue. Please help, Kipper Fletez-Brant