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.fib...@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.fib...@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 > ***=== > > ___________________________________________________________ > Please keep all replies on the list by using "reply all" > in your mail client. To manage your subscriptions to this > and other Galaxy lists, please use the interface at: > http://lists.bx.psu.edu/ > > To search Galaxy mailing lists use the unified search at: > http://galaxyproject.org/search/mailinglists/ ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
