On Mon, Feb 25, 2013 at 7:11 PM, Samuel Lampa email@example.com wrote:
I have aGalaxy toolwith some R code which is split up into a few files, which are loaded by a "master R script", which orcestrates and executes the whole thing.
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().
For future reference, queries about writing tools and extending Galaxy should go to the galaxy-dev list (CC'd), not galaxy-users.