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(a)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
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