On Mon, Feb 25, 2013 at 7:11 PM, Samuel Lampa <samuel.la...@gmail.com> wrote:
> Hi,
> 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.

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