On Fri, Apr 15, 2011 at 7:27 PM, Peter Cock <p.j.a.c...@googlemail.com>wrote:

> On Thu, Apr 14, 2011 at 2:56 PM, Leandro Hermida
> <soft...@leandrohermida.com> wrote:
> > On Thu, Apr 14, 2011 at 3:17 PM, Peter Cock <p.j.a.c...@googlemail.com>
> > wrote:
> >>
> >> For standard Python tools in Galaxy, I'm using
> >> os.path.split(sys.argv[0])[0]
> >> to get the path, which on reflection probably should be written as
> >> os.path.dirname(sys.argv[0]) as you suggest.
> >>
> >> What do __file__ and sys.argv[0] give you? The simplest way to debug
> >> this is to add a print statement, since Galaxy will show the stdout.
> >>
> >
> > Hi Peter,
> >
> > __file__ throws an error: global name '__file__' is not defined
> I guess the script is being loaded as a string, and run with eval(...)
> or something like that. It would also explain why sys.argv[0] would
> be one of the Galaxy script files.
> > os.path.abspath(os.path.dirname(sys.argv[0])) gives me
> > /path/to/galaxy/scripts directory which is two levels up from what the
> tool
> > directory I want for example /path/to/galaxy/tools/mytool
> So combine that with ../tools/mytool/ and you're done? OK, you have
> to know the name of the folder your tool *should* be in... so not a
> perfect solution.

Thanks Peter, yes that's the same idea I did as a quick fix.... also don't
like the fact that my tool directory is hard-coded but oh well.  There must
be a way within Python in Galaxy importing something from Galaxy that has
the current tool directory path, it would seem that Galaxy needs to know
this and would store it anyway?

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