Hi, thanks for the quick reply! On 02/25/2013 08:39 PM, Peter Cock wrote:
I realize that when the master script ("run.R" in my case) is run, it will >not find the other files, since it is itself moved away to a temporary >working directory (something like >".../galaxy/database/job_working_directory/000/165"). > >Is there any "standard way" of dealing with this, any special toolconfig >syntax etc? ... or do I have to just hard code the absolute paths to the >extra files in my script? :|Presumably all the child R scripts will be in the same folder as your master R script (or you know the relative path if not). So all you need to do is workout the path of the master R script, and from that compute the path to the child R scripts. I guess you can do this in R using commandArgs().
True. And yes, I do keep the other scripts in the same folder. But since the main script is moved away to the job_working_directory (but not the other scripts, as far as I can tell), they will not be in the same folder anymore, so then in order to get from the job_working_directory back to the tools folder, I would need to go something like:
[main R script folder]../../../../tools/[mytool]/r/[script file] I was thinking that it might be a bit fragile, but of course, if the directory depth of the job_working_directory path will keep quite constant it will surely not be a big problem.
For future reference, queries about writing tools and extending Galaxy should go to the galaxy-dev list (CC'd), not galaxy-users.
Ah, true! I always tend to forget that I'm not the true end-user of galaxy, although I'm in a way "using" it :)
Best Regards // Samuel ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
