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. Peter ___________________________________________________________ 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/
