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.
On Wed, May 14, 2014 at 3:37 AM, Pavel Fibich <pavel.fibich(a)prf.jcu.cz> wrote:
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
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
My galaxy instance was updated Apr 17 2014.
All the best, Pavel
Pavel Fibich pavel.fibich(a)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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