Thanks James -

I had figured out that I needed to restart the server after changing config
files, and the debug info you sent was helpful.

Thanks for taking the time to respond.


On Mon, Nov 19, 2012 at 10:38 AM, James Taylor <>wrote:

> On Fri, Nov 16, 2012 at 2:35 PM, Joshua Orvis <> wrote:
> > If I removed that line how is it still part of the call? Is Galaxy
> caching
> > the xml tool files?
> Did you restart Galaxy? Tool configuration files are read at startup.
> You can also force a tool to be reloaded in the admin interface.
> > Also, is there a way to see the precise commands being
> > executed by Galaxy for any particular tool?
> These are logged at the debug level, either to the console or
> paster.log depending on how you start Galaxy.
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