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Question: Custom Tool Output Path
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gravatar for Paul Rigor (prigor@uci)
9.3 years ago by
Paul Rigor (prigor@uci) • 50
Paul Rigor (prigor@uci) • 50 wrote:
Hi all, 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? Thanks, Paul -- Paul Rigor http://www.paulrigor.net/ http://www.ics.uci.edu/~prigor
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modified 9.3 years ago by Nate Coraor ♦ 3.2k • written 9.3 years ago by Paul Rigor (prigor@uci) • 50
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gravatar for Nate Coraor
9.3 years ago by
Nate Coraor ♦ 3.2k
United States
Nate Coraor ♦ 3.2k wrote:
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
ADD COMMENT • link written 9.3 years ago by Nate Coraor ♦ 3.2k
But in defining a tool, can the default path be overridden by assigning a different path to a variable, eg, $outputpath? Thanks, paul -- Paul Rigor http://www.paulrigor.net/ http://www.ics.uci.edu/~prigor
ADD REPLY • link written 9.3 years ago by Paul Rigor (prigor@uci) • 50
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
ADD REPLY • link written 9.3 years ago by James Taylor • 320
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