Do you have an example tool XML that is not working for you? Is it using $output.extra_files_path or $output.files_path to find this directory? My understanding is that $output.files_path outputs should be written to the working directory and the other version ($output.extra_files_path) should no longer be used in tools because of use cases like this one. If you sent me the tool though I could do some more digging and confirm this or try to correct the underlying bug if there is one. -John On Wed, May 14, 2014 at 3:37 AM, Pavel Fibich <pavel.fibich@prf.jcu.cz> wrote:

Dear developers,

my Galaxy instance runs jobs under real users (DRMAA) and is going well with small problem. external_chown script does not change owner for files specified in inputs with .files_path suffix (i.e. directory for multiple output files; seehttps://wiki.galaxyproject.org/Admin/Tools/Multiple%20Output%20Files). After the end of job, whole job_working_directory/000/NO is properly re-owned to galaxy user, but files/000/dataset_NO.files remained owned by real user and are not accessible for galaxy user. Can you help me with this problem or give me any advise?

I guess it will be something in lib/galaxy/jobs/__init__.py where re-owning is triggered.

My galaxy instance was updated Apr 17 2014.

All the best, Pavel

-- ===*** Pavel Fibich pavel.fibich@prf.jcu.cz ++420-38-777-2374 Botany, Faculty of Science, University of South Bohemia Na Zlate stoce 1, 370 05 Ceske Budejovice, Czech republic ***===

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