Hi Brad I don't you are using R to execute your R script.... How do you call your R script, ie how does the command tag looks in the tool definition file? Also, why do you have a "#!/bin/bash" at the beginning of your R script? Regards, Hans-Rudolf On 04/27/2014 09:50 PM, Bradley Belfiore wrote:

I am new to galaxy and while trying to convert an R tool to a Galaxy usable tool I keep getting: /Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1: syntax error near unexpected token `('

/Users/bmbelfio/galaxy-dist/tools/pathview/pathview.R: line 1: `args=(commandArgs(TRUE))'

any help as to how to remedy this would be greatly appreciated. The first couple lines of my .R file are # #!/bin/bash args<-(commandArgs(TRUE))

Thanks, Brad

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