On Fri, Nov 12, 2010 at 1:09 PM, Anthony Ferrari <ferraria@gmail.com> wrote:
OK. I have made some tests this morning to figure this all out. Indeed, the problem with ">" is that it catches every single message R sends to STDOUT and not only object of your interest, so this is definitely not a reliable solution. Solution suggests by Alex worked perfectly well. I would suggest also to use the 'trailingOnly=TRUE' option within the commandArgs() call in the R script. That allows you to only care about the args given after the '--args' option. You can then forget how many previous options you have in your command line (--vanilla, --slave, -f or others...). First parameter useful to your R script would then be commandArgs(trailingOnly=T)[1] and so on.
That is a very handy tip, commandArgs(trailingOnly=T), thanks!
There is just another little point that I would like to clarify. At the beginning my tests didn't work at all and I realize that I have to give the full path to the R script (in the command tag) to make it work.
What happens if you do <command> rather than <command interpreter="bash">? Peter P.S. Cross posted to Galaxy-dev, could we continue this there?