On Mon, Feb 25, 2013 at 8:02 PM, Samuel Lampa <samuel.la...@gmail.com> wrote:
> 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,
> ...

Are you just calling a pre-existing static R script, or doing something
more complicated like generating the R script in the tool XML file?
For calling pre-existing scripts or binaries, I thought it was just the
current working directory which was changed to something like


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