Paul, This would break a lot of things in Galaxy. Everything expects that a tool output is a "Dataset", and that it has a corresponding file with its contents under "file_path". Changing this would be complex and have far reaching consequences, though not impossible (on a per tool basis, the directory where the output is deposited would be changes, and the dataset would be setup pointing to the right place, however this affects how datasets get shared to the cluster among other things). Maybe it would help to better understand what you want to accomplish by doing this. (Moved to galaxy-dev since this is about framework internals not using the galaxy interface). -- jt On Aug 4, 2009, at 11:35 AM, Paul Rigor (prigor@uci) wrote:

But in defining a tool, can the default path be overridden by assigning a different path to a variable, eg, $outputpath?

Thanks, paul

On Tue, Aug 4, 2009 at 5:07 AM, Nate Coraor <nate@bx.psu.edu> wrote: Paul Rigor (prigor@uci) wrote:

For custom tools, I was wondering how the output path can be set in the xml file describing the tool? Are there 'default' variables I should be aware of in order to use as the output path the "user_library_import_dir = database/users" in my universe_wsgi.ini?

Hi Paul,

Galaxy manages output paths internally. The directory containing datasets can be changed with 'file_path' in universe_wsgi.ini. By default, it's database/files/

--nate

-- Paul Rigor http://www.paulrigor.net/ http://www.ics.uci.edu/~prigor _______________________________________________ galaxy-user mailing list galaxy-user@bx.psu.edu http://mail.bx.psu.edu/cgi-bin/mailman/listinfo/galaxy-user