[galaxy-dev] external chown does not chown multiple outputs .files_path
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; see https://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 Fibichpavel.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/
Re: [galaxy-dev] external chown does not chown multiple outputs .files_path
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 Fibichpavel.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/
Re: [galaxy-dev] external chown does not chown multiple outputs .files_path
Hi John, thank you for advise, you are right. The tool was using command interpreter=bash seqclust-main.sh -s $input -m $mvstup -o $ovstup -d $repeatmasker -v $archive -w $contigs -y $log -x pdffile.pdf -z RMSKtable -r $__root_dir__ -t $summary -u '$summary.extra_files_path' -p $paired -f $prefix -a $sq_rename -l $overlap I have removed extra_ and it starts to work. Regards, Pavel ___ 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/
