I am not using perl, but bash, which makes things much easier on the cmd line. However, maybe you know how to retrieve the R output or: what exactly is the problem for Galaxy for how to handle the system output from R through the shell? We have seen it here with other tools as well. R should work straight from the cmd line as well. And everything - incl R - does when use bash in a shell, but as soon as you put galaxy in between you and the program the output, is nowhere to be seen so far, we've been able to simply 'mv' the output from the program towards bash and that will push it to galaxy. But with R this didn't work. (so far) On 10/13/2010 12:47 PM, Leandro Hermida wrote:
Just to note for those Perl people developing tools with Galaxy and wanting to interface with R there are a couple of libraries out there to do this for you:
RSPerl http://www.omegahat.org/RSPerl/
Statistics::R http://search.cpan.org/search?query=Statistics%3A%3AR