Hi Ann we do something similar for our current NGS pipeline. We trigger the tool in Galaxy but store the data in the NGS repository. We only keep a log file as new galaxy history item. Make sure the 'user' running the galaxy server has access to this 'external' (ie non-galaxy) directory and make the corresponding changes in your scripts. Let me know if you want more details or have a look at my presentation at last year's GCC (http://wiki.galaxyproject.org/Events/GCC2011?action=AttachFile&do=get&target=SixKeyInsights.pdf slides 16 onwards) regards, Hans-Rudolf On 12/11/2012 10:04 PM, Gomez, Ann wrote:

Hi all,

I have a pipeline involving a series of scripts, which creates directories (and many subdirectories), that I’d like to wrap for use in Galaxy. Although the contents of the folders are not the primary output of the pipeline, (and I don’t want them as history items), I’d still like them to be accessible for users to double-check the contents if they so desire. However, I’m not sure where a good place to create/persist the folders would be.

Although I’m running a local install on my own machine for the moment, the goal will be to move to a cluster in the near future.

Does anyone have experience with this kind of thing or have any ideas? Apologies if I’ve missed something; I haven’t found anything related on the mailing list or the wiki, except for this thread that suggests disabling the cleanup method of the JobWrapper for debugging purposes: http://dev.list.galaxyproject.org/persisting-job-working-directory-td4138922....

Thanks for your consideration,

Ann

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