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
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